Setup: Libraries and utilities

Import data

latephase_exacer_biomarkers <- readRDS(here::here("results", "latephase_exacer_biomarkers.rds"))
load(here::here("data", "preprocessedData", "geodatasets.RDATA"))

## samples in each dataset
table(phenoDataList$GSE19301$phenotype)
## 
## EXACERBATION    FOLLOW UP        QUIET 
##          166          125          394
all(colnames(esetList$GSE19301) == rownames(phenoDataList$GSE19301))
## [1] TRUE
geoPanelGenes <- as.data.frame(t(esetList$GSE19301))
geoPanelGenes <- geoPanelGenes[, intersect(colnames(geoPanelGenes), latephase_exacer_biomarkers)]

geoPanelGenes <- add_column(geoPanelGenes, donor = phenoDataList$GSE19301$donor, .before = 1)
geoPanelGenes <- add_column(geoPanelGenes, sex = phenoDataList$GSE19301$sex, .before = 1)
geoPanelGenes <- add_column(geoPanelGenes, phenotype = phenoDataList$GSE19301$phenotype, .before = 1)

Exacerbation dataset (GSE19301)

mod_exacer <- run_lme(
  data = geoPanelGenes[phenoDataList$GSE19301$severity == "Moderate Persistent", ],
  fdr = 0.1
)
mod_exacer$severity <- "Moderate Persistent"

sev_exacer <- run_lme(
  data = geoPanelGenes[phenoDataList$GSE19301$severity == "Severe Persistent", ],
  fdr = 0.1
)
sev_exacer$severity <- "Severe Persistent"

exacer <- rbind(mod_exacer, sev_exacer)

Volcano plot (exacerbation contrasts)

scaleFUN <- function(x) sprintf("%.0f", x)

exacer$logPval <- -log10(exacer$`p-value`)
exacer$Sig <- ifelse(exacer$adj.P.Val < 0.1, "FDR<10%", "NotSignificant")

gg1 <- ggplot(exacer, aes(x = Value, y = logPval, color = Sig)) +
  geom_point(size = 2) +
  geom_vline(aes(xintercept = 0), lty = 2, color = "gray") +
  geom_text_repel(
    data = filter(exacer, adj.P.Val < 0.1),
    aes(label = feature),
    size = 2,
    max.overlaps = 100
  ) +
  customTheme(
    sizeStripFont = 8, xAngle = 0, hjust = 0.5, vjust = 0.5,
    xSize = 8, ySize = 8, xAxisSize = 8, yAxisSize = 8
  ) +
  scale_x_continuous(expression("log"[2]~"fold-change")) +
  scale_y_continuous(expression("-log"[10]~"P-value"), labels = scaleFUN) +
  scale_color_manual(values = c("blue", "gray")) +
  ggtitle("PBMCs - GSE19301") +
  theme(legend.position = "bottom") +
  facet_grid(contrast ~ severity, scales = "free")

gg1

Summarize significant hits (exacerbation)

exacer %>%
  group_by(severity, contrast, fc) %>%
  filter(adj.P.Val < 0.1) %>%
  summarise(n = n())
## # A tibble: 6 × 4
## # Groups:   severity, contrast [4]
##   severity            contrast          fc        n
##   <chr>               <chr>             <chr> <int>
## 1 Moderate Persistent Exacer - Followup UP        3
## 2 Moderate Persistent Exacer - Quiet    DOWN      1
## 3 Moderate Persistent Exacer - Quiet    UP        8
## 4 Severe Persistent   Exacer - Followup UP        1
## 5 Severe Persistent   Exacer - Quiet    DOWN      3
## 6 Severe Persistent   Exacer - Quiet    UP       11
exacer %>%
  group_by(severity, contrast, fc) %>%
  filter(adj.P.Val < 0.1) %>%
  filter(severity == "Severe Persistent", contrast == "Exacer - Quiet", fc == "DOWN") %>%
  pull(feature)
## [1] "CD48"    "C9orf78" "PABPC1"

External validation datasets (airway/blood/sputum/BALF)

select_gse <- c("GSE69683", "GSE74986", "GSE147878+GSE161245", "GSE76262+GSE147880")

result <- mapply(function(x, y, z, tis) {
  res <- test_biomarkers(eset = x, pheno = y, biomarkers = latephase_exacer_biomarkers)
  res$GSE <- z
  res$tissue <- tis
  res
},
x = esetList[select_gse],
y = phenoDataList[select_gse],
z = select_gse,
tis = sapply(phenoDataList[select_gse], function(i) unique(i$sampletype)),
SIMPLIFY = FALSE) %>%
  do.call(rbind, .) %>%
  mutate(fc = ifelse(logFC > 0, "UP", "DOWN"))

## number of patients
table(phenoDataList$GSE19301$severity, phenoDataList$GSE19301$phenotype)
##                      
##                       EXACERBATION FOLLOW UP QUIET
##   Mild Persistent                7         6    21
##   Moderate Persistent           68        60   180
##   Severe Persistent             91        59   193
length(unique(phenoDataList$GSE19301$donor[phenoDataList$GSE19301$severity == "Mild Persistent"]))
## [1] 7
length(unique(phenoDataList$GSE19301$donor[phenoDataList$GSE19301$severity == "Moderate Persistent"]))
## [1] 52
length(unique(phenoDataList$GSE19301$donor[phenoDataList$GSE19301$severity == "Severe Persistent"]))
## [1] 59
rowSums(sapply(phenoDataList[select_gse], function(i) table(i$phenotype)))
## healthyControls  moderateAsthma    severeAsthma 
##             159             171             548

GSE19301 individuals by sex and severity

phenoDataList$GSE19301 %>%
  filter(severity != "Mild Persistent") %>%
  group_by(donor) %>%
  dplyr::slice(1) %>%
  group_by(sex, severity) %>%
  summarise(n = n()) %>%
  tidyr::spread(sex, n) %>%
  mutate(total = `M` + `F`) %>%
  mutate(percent_f = 100 * signif(`F` / total, 2)) %>%
  mutate(total_percentf = paste0(total, " (", percent_f, "%)"))
## # A tibble: 2 × 6
##   severity                F     M total percent_f total_percentf
##   <chr>               <int> <int> <int>     <dbl> <chr>         
## 1 Moderate Persistent    36    16    52        69 52 (69%)      
## 2 Severe Persistent      39    20    59        66 59 (66%)

Validation datasets individuals by sex and phenotype

a <- data.frame(sampletype = sapply(phenoDataList[select_gse], function(i) unique(i$sampletype))) %>%
  mutate(gse = rownames(.))

b <- lapply(select_gse, function(i) {
  df <- as.data.frame(table(phenoDataList[[i]]$sex, phenoDataList[[i]]$phenotype))
  df$gse <- i
  df
}) %>%
  do.call(rbind, .) %>%
  tidyr::spread(Var1, Freq) %>%
  mutate(total = `F` + `M`) %>%
  mutate(percent_f = 100 * signif(`F` / total, 2))

inner_join(a, b, by = "gse") %>%
  mutate(gse_sample = paste0(sampletype, " (", gse, ")")) %>%
  mutate(total_percentf = paste0(total, " (", percent_f, "%)")) %>%
  dplyr::select(Var2, gse_sample, total_percentf) %>%
  tidyr::spread(gse_sample, total_percentf)
##              Var2 airway (GSE147878+GSE161245) balf (GSE74986) blood (GSE69683)
## 1 healthyControls                     29 (66%)        12 (42%)         87 (39%)
## 2  moderateAsthma                     23 (78%)        28 (57%)         77 (48%)
## 3    severeAsthma                     59 (63%)        46 (54%)        334 (61%)
##   induced sputum (GSE76262+GSE147880)
## 1                            31 (45%)
## 2                            43 (58%)
## 3                           109 (59%)

Volcano plots across validation datasets

df <- result %>%
  mutate(sig = -log10(P.Value)) %>%
  mutate(Significance = ifelse(adj.P.Val < 0.1, "FDR<10%", "NotSignificant")) %>%
  mutate(tissue_gse = paste(tissue, GSE, sep = "_"))

p <- df %>%
  ggplot(aes(x = logFC, y = sig, col = Significance)) +
  geom_point() +
  ggh4x::facet_grid2(vars(tissue_gse), vars(contrast),
                     scales = "free", independent = "all") +
  scale_color_manual(values = c("blue", "gray")) +
  ggrepel::geom_text_repel(
    data = subset(df, adj.P.Val < 0.1),
    aes(label = feature), size = 2, max.overlaps = 20
  ) +
  geom_vline(xintercept = 0, linetype = "dashed") +
  theme(legend.position = "top") +
  customTheme(
    sizeStripFont = 8, xAngle = 0, hjust = 0.5, vjust = 0.5,
    xSize = 8, ySize = 8, xAxisSize = 8, yAxisSize = 8
  ) +
  xlab(expression("log"[2]~"fold-change")) +
  ylab(expression("-log"[10]~"P-value"))

ggsave(
  here::here("results", "validation_of_late_phase_biomarkers_volcanoplots.png"),
  p, height = 11, width = 8
)

p

Summarize significant hits (external validation)

result %>%
  group_by(tissue, contrast, fc) %>%
  filter(adj.P.Val < 0.1) %>%
  summarise(n = n()) %>%
  tidyr::spread(fc, n)
## # A tibble: 11 × 4
## # Groups:   tissue, contrast [11]
##    tissue         contrast       DOWN    UP
##    <chr>          <chr>         <int> <int>
##  1 airway         mod - control     1     7
##  2 airway         sev - control     6    18
##  3 airway         sev - mod        NA     1
##  4 balf           mod - control     5    NA
##  5 balf           sev - control    33    33
##  6 balf           sev - mod        32    37
##  7 blood          sev - control     9    30
##  8 blood          sev - mod         3     9
##  9 induced sputum mod - control     1    NA
## 10 induced sputum sev - control    19    27
## 11 induced sputum sev - mod        17    18

Overlap of significant genes (UpSet)

sig_result <- subset(result, adj.P.Val < 0.1)
sig_exacer <- subset(exacer, adj.P.Val < 0.1)

df_exacer <- data.frame(
  panel = paste0(sig_exacer$contrast, " (", sig_exacer$severity, sig_exacer$tissue, "-", sig_exacer$GSE, ")"),
  feature = sig_exacer$feature
)

df_sev <- data.frame(
  panel = paste0(sig_result$contrast, " (", sig_result$tissue, "-", sig_result$GSE, ")"),
  feature = sig_result$feature
)

sigfeat1 <- split(df_exacer$feature, df_exacer$panel)
upset(fromList(sigfeat1), nsets = length(sigfeat1))

sigfeat2 <- split(df_sev$feature, df_sev$panel)
upset(fromList(sigfeat2), nsets = length(sigfeat2))

upset(fromList(c(sigfeat1, sigfeat2)), nsets = length(sigfeat1) + length(sigfeat2))

Exacerbation analysis

Train PLS-DA models (exacerbation)

latephase_biomarkers <- readRDS(here::here("results", "latephase_biomarkers.rds"))
latephase_biomarkers$all <- latephase_exacer_biomarkers
# exacer_plsda <- lapply(names(latephase_biomarkers), function(i){
#   biomarkers <- latephase_biomarkers[[i]]
#   ## all subjects
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_all_mod <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_all_mod$df$comparison <- paste(exacer_all_mod$df$comparison, "(Moderate Persistent)")
#   exacer_all_mod$feat$comparison <- paste(exacer_all_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_all_mod$df$sex <- exacer_all_mod$feat$sex <- "M+F"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_all_sev <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_all_sev$df$comparison <- paste(exacer_all_sev$df$comparison, "(Severe Persistent)")
#     exacer_all_sev$feat$comparison <- paste(exacer_all_sev$feat$comparison, "(Severe Persistent)")
#   exacer_all_sev$df$sex <- exacer_all_sev$feat$sex <- "M+F"
# 
#   ## females
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent" & sex ==  "F")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_f_mod <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_f_mod$df$comparison <- paste(exacer_f_mod$df$comparison, "(Moderate Persistent)")
#   exacer_f_mod$feat$comparison <- paste(exacer_f_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_f_mod$df$sex <- exacer_f_mod$feat$sex <- "F"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent" & sex ==  "F")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_f_sev <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_f_sev$df$comparison <- paste(exacer_f_sev$df$comp, "(Severe Persistent)")
#     exacer_f_sev$feat$comparison <- paste(exacer_f_sev$feat$comparison, "(Severe Persistent)")
#   exacer_f_sev$df$sex <- exacer_f_sev$feat$sex <- "F"
# 
#   ## males
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent" & sex ==  "M")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_m_mod <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_m_mod$df$comparison <- paste(exacer_m_mod$df$comparison, "(Moderate Persistent)")
#     exacer_m_mod$feat$comparison <- paste(exacer_m_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_m_mod$df$sex <- exacer_m_mod$feat$sex <- "M"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent" & sex ==  "M")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_m_sev <- multilevel_plsda(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_m_sev$df$comparison <- paste(exacer_m_sev$df$comparison, "(Severe Persistent)")
#     exacer_m_sev$feat$comparison <- paste(exacer_m_sev$feat$comparison, "(Severe Persistent)")
#   exacer_m_sev$df$sex <- exacer_m_sev$feat$sex <- "M"
# 
#   exacer_df <- rbind(exacer_all_mod$df, exacer_all_sev$df,
#                   exacer_f_mod$df, exacer_f_sev$df,
#                   exacer_m_mod$df, exacer_m_sev$df)
#   exacer_feat <- rbind(exacer_all_mod$feat, exacer_all_sev$feat,
#                 exacer_f_mod$feat, exacer_f_sev$feat,
#                 exacer_m_mod$feat, exacer_m_sev$feat)
#   exacer_df$panel <- exacer_feat$panel <- i
#   list(df = exacer_df, feat = exacer_feat)
# }) %>%
#   zip_nPure()
# saveRDS(exacer_plsda, here("results", "exacer_plsda.rds"))

Train RF models (exacerbation)

# exacer_rf <- lapply(names(latephase_biomarkers), function(i){
#   biomarkers <- latephase_biomarkers[[i]]
#   ## all subjects
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_all_mod <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers, workers = 8)
#   exacer_all_mod$df$comparison <- paste(exacer_all_mod$df$comparison , "(Moderate Persistent)")
#   exacer_all_mod$feat$comparison <- paste(exacer_all_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_all_mod$df$sex <- exacer_all_mod$feat$sex <- "M+F"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_all_sev <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_all_sev$df$comparison <- paste(exacer_all_sev$df$comparison, "(Severe Persistent)")
#   exacer_all_sev$feat$comparison <- paste(exacer_all_sev$feat$comparison, "(Severe Persistent)")
#   exacer_all_sev$df$sex <- exacer_all_sev$feat$sex <- "M+F"
# 
#   ## females
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent" & sex ==  "F")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_f_mod <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers, workers = 8)
#   exacer_f_mod$df$comparison <- paste(exacer_f_mod$df$comparison, "(Moderate Persistent)")
#   exacer_f_mod$feat$comparison <- paste(exacer_f_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_f_mod$df$sex <- exacer_f_mod$feat$sex <- "F"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent" & sex ==  "F")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_f_sev <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_f_sev$df$comparison <- paste(exacer_f_sev$df$comparison, "(Severe Persistent)")
#   exacer_f_sev$feat$comparison <- paste(exacer_f_sev$feat$comparison, "(Severe Persistent)")
#   exacer_f_sev$df$sex <- exacer_f_sev$feat$sex <- "F"
# 
#   ## males
#   demo <- subset(phenoDataList$GSE19301, severity == "Moderate Persistent" & sex ==  "M")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_m_mod <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers, workers = 8)
#   exacer_m_mod$df$comparison <- paste(exacer_m_mod$df$comparison, "(Moderate Persistent)")
#   exacer_m_mod$feat$comparison <- paste(exacer_m_mod$feat$comparison, "(Moderate Persistent)")
#   exacer_m_mod$df$sex <- exacer_m_mod$feat$sex <- "M"
#   demo <- subset(phenoDataList$GSE19301, severity == "Severe Persistent" & sex ==  "M")
#   eset <- esetList$GSE19301[intersect(rownames(esetList$GSE19301), biomarkers), rownames(demo)]
#   exacer_m_sev <- multilevel_rf(eset = eset, demo = demo,
#                    biomarkers = biomarkers)
#   exacer_m_sev$df$comparison <- paste(exacer_m_sev$df$comparison, "(Severe Persistent)")
#   exacer_m_sev$feat$comparison <- paste(exacer_m_sev$feat$comparison, "(Severe Persistent)")
#   exacer_m_sev$df$sex <- exacer_m_sev$feat$sex <- "M"
# 
#   exacer_df <- rbind(exacer_all_mod$df, exacer_all_sev$df,
#                   exacer_f_mod$df, exacer_f_sev$df,
#                   exacer_m_mod$df, exacer_m_sev$df)
#   exacer_feat <- rbind(exacer_all_mod$feat, exacer_all_sev$feat,
#                 exacer_f_mod$feat, exacer_f_sev$feat,
#                 exacer_m_mod$feat, exacer_m_sev$feat)
#   exacer_df$panel <- exacer_feat$panel <- i
#   list(df = exacer_df, feat = exacer_feat)
# }) %>%
#   zip_nPure()
# saveRDS(exacer_rf, here("results", "exacer_rf.rds"))

Plot model performance heatmap (exacerbation)

exacer_plsda <- readRDS(here("results", "exacer_plsda.rds"))
exacer_rf <- readRDS(here("results", "exacer_rf.rds"))
col_names <- intersect(colnames(exacer_rf$df[[1]]), colnames(exacer_plsda$df[[1]]))
panel_names <- c("all", "panCancer", "UCSC_isoforms", "UCSC", "Ensembl", "Trinity")
auc <- rbind(do.call(rbind, exacer_rf$df),
             do.call(rbind, exacer_plsda$df))[, col_names] %>% 
  filter(stat == "AUC.mean") %>% 
  dplyr::select(-stat) %>% 
  mutate(model_panel = paste(model, panel, sep="_")) %>% 
  dplyr::select(-c(model, panel)) %>% 
  spread(model_panel, value)

auc2 <- auc[, -c(1:4)]
classifer <- factor(sapply(strsplit(colnames(auc2), "_"), function(i) i[[1]]),
                    c("RF", "PLSDA"))
colnames(auc2) <- sapply(strsplit(colnames(auc2), "_"), function(i) i[[2]])
row_ha <- rowAnnotation(sampletype=rep("PBMCs", nrow(auc)),
                        comparison=auc$comparison, 
                        sex=auc$sex,
                        col = list(sampletype = c("PBMCs" = "red"),
                                   comparison = c("Exacer vs. Quiet (Moderate Persistent)"="#DEEBF7", "Exacer vs. Quiet (Severe Persistent)"="#9ECAE1", "Exacer vs. followup (Moderate Persistent)"="#4292C6", "Exacer vs. followup (Severe Persistent)"="#084594"),
                                   sex = c("F"="#80CDC1","M"="#35978F","M+F"="#01665E")))

h1 <- Heatmap(auc2, column_split = classifer,
        right_annotation = row_ha, 
        cluster_columns = TRUE,
        border = TRUE, name="AUC",
    cell_fun = function(j, i, x, y, width, height, fill) {
        if(auc2[i, j] > 0.9) {
          grid.text("***", x, y, gp = gpar(fontsize = 15))
        } else if(auc2[i, j] > 0.8) {
          grid.text("**", x, y, gp = gpar(fontsize = 15))
        } else if(auc2[i, j] > 0.7) {
          grid.text("*", x, y, gp = gpar(fontsize = 15))
        }
})
h1

Summarize model performance table (exacerbation)

exacertable <- rbind(do.call(rbind, exacer_plsda$df)[, col_names], 
                     do.call(rbind, exacer_rf$df)[, col_names]) %>% 
  mutate(value = signif(value, 2)) %>%  
  filter(stat == "AUC.mean") %>% 
  spread(model, value) %>% 
  filter(PLSDA > 0.7) %>% 
  filter(RF > 0.7)
write.csv(exacertable, here::here("results", "exacerbation_models_perfs.csv"))

knitr::kable(exacertable)
gse sampletype comparison stat sex panel PLSDA RF
GSE19301 blood Exacer vs. followup (Moderate Persistent) AUC.mean M all 0.96 0.87
GSE19301 blood Exacer vs. followup (Moderate Persistent) AUC.mean M Ensembl 0.89 0.76
GSE19301 blood Exacer vs. followup (Moderate Persistent) AUC.mean M panCancer 0.94 0.85
GSE19301 blood Exacer vs. followup (Moderate Persistent) AUC.mean M Trinity 0.88 0.89
GSE19301 blood Exacer vs. followup (Moderate Persistent) AUC.mean M UCSC 0.96 0.83
GSE19301 blood Exacer vs. followup (Moderate Persistent) AUC.mean M UCSC_isoforms 0.88 0.84
GSE19301 blood Exacer vs. followup (Moderate Persistent) AUC.mean M+F all 0.79 0.75
GSE19301 blood Exacer vs. followup (Moderate Persistent) AUC.mean M+F panCancer 0.75 0.71
GSE19301 blood Exacer vs. followup (Moderate Persistent) AUC.mean M+F UCSC_isoforms 0.71 0.71
GSE19301 blood Exacer vs. followup (Severe Persistent) AUC.mean M all 0.84 0.71
GSE19301 blood Exacer vs. followup (Severe Persistent) AUC.mean M Ensembl 0.76 0.73
GSE19301 blood Exacer vs. followup (Severe Persistent) AUC.mean M+F panCancer 0.76 0.71
GSE19301 blood Exacer vs. Quiet (Severe Persistent) AUC.mean M all 0.85 0.74
GSE19301 blood Exacer vs. Quiet (Severe Persistent) AUC.mean M Ensembl 0.83 0.77
GSE19301 blood Exacer vs. Quiet (Severe Persistent) AUC.mean M UCSC 0.82 0.74

Compile feature importance (exacerbation)

selectcols <- intersect(colnames(exacer_plsda$feat[[1]]), colnames(exacer_rf$feat[[1]]))
exacerfeat <- rbind(do.call(rbind, exacer_plsda$feat)[, selectcols], 
                     do.call(rbind, exacer_rf$feat)[,selectcols]) %>% 
  right_join(exacertable, by=c("gse", "comparison", "panel", "sex")) %>% 
  dplyr::select(-c(stat, PLSDA, RF, sampletype, gse)) %>% 
  group_by(comparison, panel, sex, model) %>%
  mutate(rank_pct = percent_rank(importance))

knitr::kable(exacerfeat)
importance feature comparison model sex panel rank_pct
0.0877911 ABHD5 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.0000000
1.0224415 AHCTF1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.6923077
0.8704903 ATP8A1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.5000000
0.5661089 C9orf78 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.1538462
0.9756409 CARM1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.6153846
1.1376971 CASP8 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.7307692
0.8850023 CD4 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.5384615
1.5128511 CD8A Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.8846154
1.0104758 CLEC4E Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.6538462
0.5715329 DAP Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.1923077
0.1768168 F13A1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.0384615
0.6461579 FAM8A1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.2692308
1.3216195 FOS Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.8076923
0.8166068 FUT7 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.4230769
1.3525909 GNLY Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.8461538
1.7056172 KRT23 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.9615385
0.6704963 LMBRD1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.3461538
1.7079546 NAPA Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 1.0000000
0.6488016 NFKBIA Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.3076923
1.6797881 PABPC1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.9230769
0.6715769 PPP3R1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.3846154
0.2661511 RGS2 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.0769231
0.8869331 SF3B1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.5769231
0.8357684 SH3BGRL3 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.4615385
1.2294257 SULT1A1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.7692308
0.3651834 TGFBI Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.1153846
0.5836783 ZNF185 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC 0.2307692
0.4473591 ABHD5 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.1923077
1.1174415 AHCTF1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.6923077
1.4319774 ATP8A1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.9615385
1.0028204 C9orf78 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.5000000
1.0169405 CARM1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.5384615
0.3413159 CASP8 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.1153846
0.3866290 CD4 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.1538462
1.2426199 CD8A Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.7692308
1.0991658 CLEC4E Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.6538462
1.0174478 DAP Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.5769231
0.1737126 F13A1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.0384615
0.5793715 FAM8A1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.3461538
0.4692968 FOS Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.2307692
0.8601632 FUT7 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.4615385
1.3797764 GNLY Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.8846154
0.5694985 KRT23 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.3076923
1.3781785 LMBRD1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.8461538
2.0901844 NAPA Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 1.0000000
0.1372844 NFKBIA Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.0000000
1.2580091 PABPC1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.8076923
0.8493250 PPP3R1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.4230769
0.4702369 RGS2 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.2692308
1.4029497 SF3B1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.9230769
1.2140191 SH3BGRL3 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.7307692
0.5982879 SULT1A1 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.3846154
0.2372827 TGFBI Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.0769231
1.0884730 ZNF185 Exacer vs. Quiet (Severe Persistent) PLSDA M UCSC 0.6153846
0.1803827 ATP11A Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.0000000
0.5640095 ATP8A1 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.1785714
0.5872002 CD8A Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.2142857
0.8403073 CLEC4E Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.5000000
1.5279153 COPB1 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.9285714
0.4505025 F13A1 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.1428571
0.2447460 FAM8A1 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.0357143
1.1248206 FPR2 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.7142857
1.4593048 GNAS Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.8928571
2.1129936 GNLY Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 1.0000000
1.4006469 IL1R2 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.8571429
0.9609346 MAP3K8 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.6428571
0.6829335 MME Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.4285714
1.7815826 NAPA Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.9642857
0.9417063 NFKBIA Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.5714286
1.2480459 PELI1 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.8214286
1.1601356 PLXNC1 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.7500000
0.6750556 PTPN18 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.3928571
0.5990098 QKI Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.2500000
0.6417218 RGS2 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.3214286
0.2510591 SEMA4D Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.0714286
0.6748342 SF3B1 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.3571429
0.9452884 SH3BGRL3 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.6071429
1.1813716 SULT1A1 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.7857143
0.6936612 TGFBI Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.4642857
0.6195848 TIA1 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.2857143
0.4245471 VCAN Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.1071429
0.8913275 VPS13A Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.5357143
0.9756126 ZNF609 Exacer vs. followup (Moderate Persistent) PLSDA M+F UCSC_isoforms 0.6785714
0.4020223 ATP11A Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.1071429
0.8860436 ATP8A1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.5357143
1.4396901 CD8A Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.8571429
1.3512213 CLEC4E Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.7500000
1.8213609 COPB1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 1.0000000
0.2735740 F13A1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.0357143
0.6867574 FAM8A1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.4642857
1.4790375 FPR2 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.8928571
0.9515987 GNAS Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.6428571
1.3879264 GNLY Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.8214286
0.3212753 IL1R2 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.0714286
0.2353370 MAP3K8 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.0000000
0.6838714 MME Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.4285714
1.7293257 NAPA Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.9642857
0.6415576 NFKBIA Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.3571429
0.5505922 PELI1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.2857143
1.6903877 PLXNC1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.9285714
0.9285497 PTPN18 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.5714286
0.9305672 QKI Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.6071429
0.4196255 RGS2 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.1785714
0.6539878 SEMA4D Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.3928571
0.9691715 SF3B1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.6785714
0.8172215 SH3BGRL3 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.5000000
1.3625132 SULT1A1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.7857143
0.6012095 TGFBI Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.3214286
0.4197238 TIA1 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.2142857
1.1482195 VCAN Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.7142857
0.4099388 VPS13A Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.1428571
0.5127518 ZNF609 Exacer vs. followup (Moderate Persistent) PLSDA M UCSC_isoforms 0.2500000
0.9300874 AHCTF1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.5714286
0.9322525 ATP8A1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.6071429
0.5490593 C9orf78 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.2500000
0.7076325 CARM1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.3571429
1.3594702 CD8A Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.8571429
0.3741793 CHP1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.1785714
1.0960742 CISH Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.7142857
0.9440011 CLEC4E Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.6428571
0.7665829 CTDSP2 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.4285714
1.8921714 CTSA Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 1.0000000
0.7512955 DAP Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.3928571
0.3160528 DESI1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.0714286
0.3474527 F13A1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.1071429
0.9008612 FAM8A1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.5357143
0.3685283 GBE1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.1428571
1.4086930 GNLY Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.8928571
0.6304071 ITSN1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.2857143
1.3206876 KIAA1551 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.8214286
1.8776638 KRT23 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.9642857
1.6509880 PABPC1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.9285714
0.6843379 PPP3R1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.3214286
0.8862552 RALGPS2 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.5000000
0.1448315 RGS2 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.0000000
1.2038069 SF3B1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.7857143
1.1198763 SH3BGRL3 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.7500000
1.0751600 SMCHD1 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.6785714
0.8067201 TGFBI Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.4642857
0.1788827 ZNF185 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.0357143
0.5369857 ZNF281 Exacer vs. followup (Moderate Persistent) PLSDA M Ensembl 0.2142857
1.2834740 AHCTF1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.8214286
1.3257733 ATP8A1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.8928571
0.9523216 C9orf78 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.5357143
0.9401382 CARM1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.5000000
1.1576029 CD8A Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.7857143
0.5597433 CHP1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.1428571
1.3892372 CISH Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.9285714
1.1540047 CLEC4E Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.7500000
0.7630767 CTDSP2 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.2500000
1.7030912 CTSA Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 1.0000000
0.9897867 DAP Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.5714286
1.0259112 DESI1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.6071429
0.5028171 F13A1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.0714286
0.5404799 FAM8A1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.1071429
0.0651958 GBE1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.0000000
1.4518977 GNLY Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.9642857
0.9324425 ITSN1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.4642857
0.8592535 KIAA1551 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.3928571
0.6765841 KRT23 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.2142857
1.1516170 PABPC1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.7142857
0.7905629 PPP3R1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.3571429
0.7736266 RALGPS2 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.3214286
0.4888772 RGS2 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.0357143
1.3149607 SF3B1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.8571429
1.1181224 SH3BGRL3 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.6785714
0.8709182 SMCHD1 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.4285714
0.6035202 TGFBI Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.1785714
1.0813882 ZNF185 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.6428571
0.7689633 ZNF281 Exacer vs. Quiet (Severe Persistent) PLSDA M Ensembl 0.2857143
0.4067022 AHCTF1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.1071429
1.2605809 ATP8A1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.7500000
1.5819286 C9orf78 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.9642857
0.9918346 CARM1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.5714286
0.8202338 CD8A Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.4285714
0.8173274 CHP1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.3928571
1.9415268 CISH Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 1.0000000
1.0311537 CLEC4E Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.6428571
0.7635236 CTDSP2 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.3214286
1.3214434 CTSA Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.8571429
1.0364489 DAP Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.7142857
0.9025835 DESI1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.5000000
1.4055280 F13A1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.8928571
1.2712943 FAM8A1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.7857143
0.0822397 GBE1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.0357143
0.5296847 GNLY Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.2142857
0.9617249 ITSN1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.5357143
0.3402024 KIAA1551 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.0714286
0.7863603 KRT23 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.3571429
0.4676326 PABPC1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.1428571
0.4964051 PPP3R1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.1785714
0.7052919 RALGPS2 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.2857143
0.8707276 RGS2 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.4642857
1.0331844 SF3B1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.6785714
1.2816592 SH3BGRL3 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.8214286
0.9941773 SMCHD1 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.6071429
0.6436201 TGFBI Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.2500000
1.4126411 ZNF185 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.9285714
0.0237509 ZNF281 Exacer vs. followup (Severe Persistent) PLSDA M Ensembl 0.0000000
0.9174632 CASP8 Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 0.5555556
1.4732724 CECR1 Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 1.0000000
0.6469333 FPR1 Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 0.1111111
1.1591063 FPR2 Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 0.7777778
0.5502773 IFRD1 Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 0.0000000
1.0868191 LYST Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 0.6666667
0.9111520 QKI Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 0.4444444
1.2410676 SETX Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 0.8888889
0.7381732 SF3B1 Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 0.2222222
0.9090393 TNFRSF10C Exacer vs. followup (Moderate Persistent) PLSDA M Trinity 0.3333333
1.0169273 ARG2 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.6216216
1.2071914 CD48 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.7837838
0.6053159 CD55 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.1621622
1.0147593 CDH1 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.5945946
0.1807212 CREBBP Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.0270270
0.8052270 CXCL10 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.3783784
0.7140808 CXCL2 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.3243243
0.6862511 CXCL6 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.2432432
0.8046177 F13A1 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.3513514
0.7063260 FOS Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.2972973
1.2598111 FOXJ1 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.8378378
0.6010383 FUT7 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.1351351
1.8672136 IFI35 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 1.0000000
0.8532260 IL15RA Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.4324324
0.8587806 IL1R1 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.4864865
0.6996183 IL26 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.2702703
1.3180710 IL32 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.8918919
1.2273357 ITGA2B Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.8108108
1.1491755 JAM3 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.7567568
0.9253242 LCN2 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.5675676
1.4943660 LCP1 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.9189189
1.6254987 LILRB1 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.9729730
0.6849084 MAP3K5 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.2162162
1.0272311 MS4A2 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.6486486
0.5688267 PLAU Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.1081081
1.0892099 PPBP Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.6756757
0.5571441 PSEN1 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.0540541
1.0930164 SBNO2 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.7027027
1.1001293 SELPLG Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.7297297
0.8591867 SH2B2 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.5135135
0.8958020 SPINK5 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.5405405
0.1544993 TFEB Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.0000000
1.3172065 TFRC Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.8648649
0.5669270 THY1 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.0810811
0.8313618 TLR7 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.4054054
1.5350921 TNFSF10 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.9459459
0.8569296 TNFSF4 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.4594595
0.6825752 ULBP2 Exacer vs. followup (Moderate Persistent) PLSDA M+F panCancer 0.1891892
1.5383153 ARG2 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.8648649
1.1829750 CD48 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.7837838
0.5050695 CD55 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.2432432
0.5979769 CDH1 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.3513514
0.6784124 CREBBP Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.4324324
1.0312915 CXCL10 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.6486486
0.2558693 CXCL2 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.1081081
0.1145380 CXCL6 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.0000000
1.0908750 F13A1 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.7027027
0.9911977 FOS Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.6216216
0.5801083 FOXJ1 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.2972973
0.5671567 FUT7 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.2702703
1.0628298 IFI35 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.6756757
0.7460665 IL15RA Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.4864865
0.2374816 IL1R1 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.0810811
0.7322161 IL26 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.4594595
0.4319631 IL32 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.2162162
0.7879571 ITGA2B Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.5675676
0.2118370 JAM3 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.0540541
2.2212908 LCN2 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 1.0000000
0.9536251 LCP1 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.5945946
1.7285613 LILRB1 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.9729730
0.3035852 MAP3K5 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.1351351
0.1551969 MS4A2 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.0270270
0.7653851 PLAU Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.5405405
1.1125762 PPBP Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.7297297
0.3874246 PSEN1 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.1891892
1.7025763 SBNO2 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.9189189
0.3612447 SELPLG Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.1621622
1.6288792 SH2B2 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.8918919
0.5829659 SPINK5 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.3243243
0.6451082 TFEB Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.4054054
1.7127206 TFRC Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.9459459
0.7614964 THY1 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.5135135
1.4117139 TLR7 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.8378378
1.1451823 TNFSF10 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.7567568
1.2124262 TNFSF4 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.8108108
0.6400770 ULBP2 Exacer vs. followup (Severe Persistent) PLSDA M+F panCancer 0.3783784
1.1826808 ARG2 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.7027027
0.5123010 CD48 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.1891892
0.3896840 CD55 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.1351351
0.9606092 CDH1 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.5135135
0.4009437 CREBBP Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.1621622
1.0873882 CXCL10 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.6216216
0.3559479 CXCL2 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.1081081
1.7464995 CXCL6 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 1.0000000
0.6885290 F13A1 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.3783784
1.0974646 FOS Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.6486486
0.2612269 FOXJ1 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.0540541
0.5738559 FUT7 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.2972973
1.6778245 IFI35 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.9729730
0.6589128 IL15RA Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.3513514
0.1386748 IL1R1 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.0000000
1.4289972 IL26 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.8918919
0.8784814 IL32 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.4864865
1.0134434 ITGA2B Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.5675676
1.1221671 JAM3 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.6756757
0.5299687 LCN2 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.2162162
1.6440995 LCP1 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.9459459
1.3461723 LILRB1 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.8378378
0.6111722 MAP3K5 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.3243243
1.0228056 MS4A2 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.5945946
0.2552212 PLAU Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.0270270
0.9886653 PPBP Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.5405405
1.2520930 PSEN1 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.7837838
0.8627602 SBNO2 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.4594595
1.4764003 SELPLG Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.9189189
1.4004986 SH2B2 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.8648649
1.2001291 SPINK5 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.7297297
1.2407031 TFEB Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.7567568
0.5725011 TFRC Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.2702703
0.5388196 THY1 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.2432432
0.2722379 TLR7 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.0810811
1.2729485 TNFSF10 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.8108108
0.8550295 TNFSF4 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.4324324
0.7513250 ULBP2 Exacer vs. followup (Moderate Persistent) PLSDA M panCancer 0.4054054
0.6044210 ABHD5 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2127660
0.6837999 AHCTF1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2978723
0.7130663 ARG2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.3404255
0.0269865 ATP11A Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0000000
0.4327256 ATP8A1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0957447
0.8602907 C9orf78 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.4680851
0.6094054 CARM1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2234043
0.6475334 CASP8 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2659574
0.9392675 CD4 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5638298
0.9967116 CD48 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.6170213
1.1626274 CD55 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7978723
0.5072926 CD8A Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.1489362
1.0697222 CDH1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7446809
1.8910084 CECR1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.9893617
1.0658100 CHP1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7340426
0.6030846 CISH Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.1914894
0.8494652 CLEC4E Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.4468085
1.1104248 COPB1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7765957
0.3306227 CREBBP Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0531915
1.8500108 CTDSP2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.9680851
1.4534347 CTSA Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.8936170
1.0021742 CXCL10 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.6382979
1.0620763 CXCL2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7234043
0.7110702 CXCL6 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.3297872
0.4371152 DAP Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.1063830
0.8231883 DESI1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.4255319
0.4559994 F13A1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.1170213
0.2864787 FAM8A1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0319149
0.8739648 FOS Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.4893617
1.4466114 FOXJ1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.8829787
0.8722879 FPR1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.4787234
0.8900180 FPR2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5319149
0.6889401 FUT7 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.3085106
1.2069016 GBE1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.8191489
1.2200048 GNAS Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.8297872
1.5459320 GNLY Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.9148936
2.1454943 IFI35 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 1.0000000
1.0442114 IFRD1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.6914894
0.8379855 IL15RA Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.4361702
1.0815916 IL1R1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7553191
1.0600990 IL1R2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7127660
0.7562684 IL26 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.3723404
1.4628293 IL32 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.9042553
0.8915369 ITGA2B Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5425532
0.1902779 ITSN1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0106383
1.1751169 JAM3 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.8085106
0.6914221 KIAA1551 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.3191489
0.8753571 KRT23 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5106383
1.0570349 LCN2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7021277
1.7247584 LCP1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.9468085
1.8729356 LILRB1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.9787234
0.8832964 LMBRD1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5212766
0.9971940 LYST Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.6276596
0.6709763 MAP3K5 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2765957
0.8743412 MAP3K8 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5000000
0.9522570 MME Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5851064
1.1586116 MS4A2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7872340
1.2942396 NAPA Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.8510638
0.6835923 NFKBIA Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2872340
0.8092696 PABPC1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.4148936
1.3775667 PELI1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.8617021
0.4810959 PLAU Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.1276596
0.9093989 PLXNC1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5531915
0.9565624 PPBP Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5957447
1.2898648 PPP3R1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.8404255
0.6138724 PSEN1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2340426
0.4841938 PTPN18 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.1382979
0.6442788 QKI Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2553191
0.5483505 RALGPS2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.1702128
0.2749511 RGS2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0212766
0.8549743 SBNO2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.4574468
1.3819360 SELPLG Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.8723404
0.3111912 SEMA4D Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0425532
1.0026812 SETX Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.6489362
0.6277688 SF3B1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2446809
1.0292575 SH2B2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.6702128
0.7606755 SH3BGRL3 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.3829787
0.4294031 SMCHD1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0851064
0.9633167 SPINK5 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.6063830
1.6740658 SULT1A1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.9361702
0.3930779 TFEB Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0638298
1.5923144 TFRC Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.9255319
0.9433092 TGFBI Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.5744681
0.5724803 THY1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.1808511
0.7471686 TIA1 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.3617021
0.8033264 TLR7 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.4042553
0.5304054 TNFRSF10C Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.1595745
1.7451465 TNFSF10 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.9574468
1.0225948 TNFSF4 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.6595745
0.8031226 ULBP2 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.3936170
1.0929130 VCAN Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.7659574
1.0435171 VPS13A Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.6808511
0.4280681 ZNF185 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.0744681
0.6032667 ZNF281 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.2021277
0.7352649 ZNF609 Exacer vs. followup (Moderate Persistent) PLSDA M+F all 0.3510638
0.1396135 ABHD5 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0106383
0.7988486 AHCTF1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.4893617
0.9629611 ARG2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5957447
0.3828564 ATP11A Exacer vs. followup (Moderate Persistent) PLSDA M all 0.1276596
0.8129386 ATP8A1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5000000
0.7589839 C9orf78 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.4574468
0.5658763 CARM1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2978723
1.1343572 CASP8 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.6808511
0.9687863 CD4 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.6063830
0.5373278 CD48 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2765957
0.4153636 CD55 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.1489362
1.3508601 CD8A Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7872340
1.2495845 CDH1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7446809
1.6373619 CECR1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.9361702
0.4919764 CHP1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2234043
0.9949460 CISH Exacer vs. followup (Moderate Persistent) PLSDA M all 0.6382979
0.9765410 CLEC4E Exacer vs. followup (Moderate Persistent) PLSDA M all 0.6170213
1.6237651 COPB1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.9255319
0.6527438 CREBBP Exacer vs. followup (Moderate Persistent) PLSDA M all 0.3829787
0.1897557 CTDSP2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0212766
1.6692665 CTSA Exacer vs. followup (Moderate Persistent) PLSDA M all 0.9680851
1.2278565 CXCL10 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7340426
0.2870357 CXCL2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0744681
1.9121852 CXCL6 Exacer vs. followup (Moderate Persistent) PLSDA M all 1.0000000
0.5108992 DAP Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2446809
0.4934947 DESI1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2340426
0.2259296 F13A1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0425532
0.5907349 FAM8A1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.3297872
1.1839824 FOS Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7127660
0.2305321 FOXJ1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0531915
0.6358279 FPR1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.3723404
1.3552043 FPR2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7978723
0.5939792 FUT7 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.3404255
0.3359563 GBE1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.1063830
1.0121174 GNAS Exacer vs. followup (Moderate Persistent) PLSDA M all 0.6489362
1.2552978 GNLY Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7659574
1.8597532 IFI35 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.9893617
1.0908055 IFRD1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.6595745
0.8887007 IL15RA Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5638298
0.0622729 IL1R1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0000000
0.5354975 IL1R2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2553191
1.6402085 IL26 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.9468085
0.9484873 IL32 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5851064
0.7095413 ITGA2B Exacer vs. followup (Moderate Persistent) PLSDA M all 0.4255319
0.4630814 ITSN1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.1914894
1.2648564 JAM3 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7765957
1.1010261 KIAA1551 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.6702128
1.5683017 KRT23 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.8936170
0.3102065 LCN2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0957447
1.8189911 LCP1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.9787234
1.6532161 LILRB1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.9574468
0.4839587 LMBRD1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2127660
1.2496831 LYST Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7553191
0.6713329 MAP3K5 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.3936170
0.5367220 MAP3K8 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2659574
0.7184775 MME Exacer vs. followup (Moderate Persistent) PLSDA M all 0.4361702
1.3696782 MS4A2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.8085106
1.5681780 NAPA Exacer vs. followup (Moderate Persistent) PLSDA M all 0.8829787
0.5840851 NFKBIA Exacer vs. followup (Moderate Persistent) PLSDA M all 0.3191489
1.4967716 PABPC1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.8723404
0.8705394 PELI1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5531915
0.2168806 PLAU Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0319149
1.4579771 PLXNC1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.8617021
0.9394627 PPBP Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5744681
0.6184122 PPP3R1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.3510638
1.4233356 PSEN1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.8191489
0.8628199 PTPN18 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5212766
1.1437896 QKI Exacer vs. followup (Moderate Persistent) PLSDA M all 0.6914894
0.7453109 RALGPS2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.4468085
0.2739491 RGS2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0638298
0.7866759 SBNO2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.4787234
1.5888118 SELPLG Exacer vs. followup (Moderate Persistent) PLSDA M all 0.9148936
0.5639124 SEMA4D Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2872340
1.4487128 SETX Exacer vs. followup (Moderate Persistent) PLSDA M all 0.8510638
0.8672363 SF3B1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5319149
1.5688750 SH2B2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.9042553
0.8387953 SH3BGRL3 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5106383
0.8683161 SMCHD1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.5425532
1.4486471 SPINK5 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.8404255
1.2168380 SULT1A1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7234043
1.1455468 TFEB Exacer vs. followup (Moderate Persistent) PLSDA M all 0.7021277
0.4461446 TFRC Exacer vs. followup (Moderate Persistent) PLSDA M all 0.1702128
0.6214079 TGFBI Exacer vs. followup (Moderate Persistent) PLSDA M all 0.3617021
0.5731580 THY1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.3085106
0.3866741 TIA1 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.1382979
0.4349756 TLR7 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.1595745
0.7644404 TNFRSF10C Exacer vs. followup (Moderate Persistent) PLSDA M all 0.4680851
1.4457916 TNFSF10 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.8297872
0.6889863 TNFSF4 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.4042553
0.6954569 ULBP2 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.4148936
0.9925742 VCAN Exacer vs. followup (Moderate Persistent) PLSDA M all 0.6276596
0.3646689 VPS13A Exacer vs. followup (Moderate Persistent) PLSDA M all 0.1170213
0.3001418 ZNF185 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.0851064
0.4745299 ZNF281 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.2021277
0.4624202 ZNF609 Exacer vs. followup (Moderate Persistent) PLSDA M all 0.1808511
0.5124642 ABHD5 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2340426
1.1954733 AHCTF1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.6914894
1.3586989 ARG2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.8617021
0.9113406 ATP11A Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.4893617
1.3225016 ATP8A1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.8191489
1.2422778 C9orf78 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7659574
0.9164864 CARM1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5000000
0.4293502 CASP8 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.1914894
0.2677468 CD4 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.1063830
1.5733992 CD48 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.9574468
1.3264908 CD55 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.8297872
1.2012063 CD8A Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7127660
0.2117935 CDH1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0744681
1.1135317 CECR1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.6489362
0.4714383 CHP1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2127660
1.4405875 CISH Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.9042553
1.7132021 CLEC4E Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.9893617
1.5494814 COPB1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.9468085
0.2004943 CREBBP Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0638298
0.6405551 CTDSP2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2978723
1.7007884 CTSA Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.9787234
1.1385226 CXCL10 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.6702128
0.7464985 CXCL2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.3404255
0.3733400 CXCL6 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.1595745
0.9520121 DAP Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5319149
1.0008131 DESI1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5531915
0.2153429 F13A1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0851064
0.8596094 FAM8A1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.4468085
0.4961778 FOS Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2234043
0.2709366 FOXJ1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.1170213
1.3468404 FPR1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.8510638
1.2411751 FPR2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7553191
1.2004327 FUT7 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7021277
0.0454819 GBE1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0000000
1.2023492 GNAS Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7234043
1.2823566 GNLY Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7872340
1.3877940 IFI35 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.8723404
0.6289623 IFRD1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2872340
0.7617012 IL15RA Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.3723404
0.8368780 IL1R1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.4255319
1.1057004 IL1R2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.6382979
0.7562368 IL26 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.3617021
0.0815110 IL32 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0106383
0.8686432 ITGA2B Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.4574468
1.0164793 ITSN1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5744681
0.7829783 JAM3 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.3936170
0.5450374 KIAA1551 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2553191
1.0704684 KRT23 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.6063830
0.9061781 LCN2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.4787234
1.0489841 LCP1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5957447
1.4659739 LILRB1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.9255319
1.4155443 LMBRD1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.8829787
0.2617321 LYST Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0957447
0.6008090 MAP3K5 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2765957
0.7647225 MAP3K8 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.3829787
1.0021588 MME Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5638298
0.4556744 MS4A2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2021277
1.9707302 NAPA Exacer vs. Quiet (Severe Persistent) PLSDA M all 1.0000000
0.7542995 NFKBIA Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.3510638
1.4430928 PABPC1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.9148936
0.6518819 PELI1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.3191489
1.3191707 PLAU Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.8085106
1.1806643 PLXNC1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.6808511
0.1454084 PPBP Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0212766
0.9379708 PPP3R1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5212766
0.5321064 PSEN1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2446809
0.5938977 PTPN18 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.2659574
0.8477099 QKI Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.4361702
0.8177827 RALGPS2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.4148936
0.4050841 RGS2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.1808511
1.6342169 SBNO2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.9680851
0.9624975 SELPLG Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5425532
0.3154286 SEMA4D Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.1276596
1.0749971 SETX Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.6170213
1.4275942 SF3B1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.8936170
1.5413017 SH2B2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.9361702
1.0986191 SH3BGRL3 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.6276596
0.3615408 SMCHD1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.1489362
0.8156305 SPINK5 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.4042553
0.8844474 SULT1A1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.4680851
1.2344294 TFEB Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7340426
1.2510662 TFRC Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7765957
0.1558861 TGFBI Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0319149
0.1976275 THY1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0531915
1.1309605 TIA1 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.6595745
0.3871843 TLR7 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.1702128
1.3410333 TNFRSF10C Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.8404255
1.2898611 TNFSF10 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7978723
0.9345289 TNFSF4 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5106383
0.7417396 ULBP2 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.3297872
0.6496905 VCAN Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.3085106
0.1969074 VPS13A Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.0425532
1.0343398 ZNF185 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.5851064
1.2348253 ZNF281 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.7446809
0.3265706 ZNF609 Exacer vs. Quiet (Severe Persistent) PLSDA M all 0.1382979
1.3484016 ABHD5 Exacer vs. followup (Severe Persistent) PLSDA M all 0.8510638
0.4478972 AHCTF1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.1382979
1.4218162 ARG2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.9042553
0.7456570 ATP11A Exacer vs. followup (Severe Persistent) PLSDA M all 0.3617021
1.2660754 ATP8A1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.7446809
1.5631292 C9orf78 Exacer vs. followup (Severe Persistent) PLSDA M all 0.9468085
1.0959739 CARM1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.6595745
1.0095342 CASP8 Exacer vs. followup (Severe Persistent) PLSDA M all 0.5957447
0.1400973 CD4 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0319149
1.3057807 CD48 Exacer vs. followup (Severe Persistent) PLSDA M all 0.8297872
0.3049016 CD55 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0744681
0.6834716 CD8A Exacer vs. followup (Severe Persistent) PLSDA M all 0.3085106
1.4330091 CDH1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.9148936
1.3502096 CECR1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.8617021
0.6727582 CHP1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.2765957
2.0308699 CISH Exacer vs. followup (Severe Persistent) PLSDA M all 1.0000000
1.4131070 CLEC4E Exacer vs. followup (Severe Persistent) PLSDA M all 0.8936170
1.3446453 COPB1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.8404255
1.0877906 CREBBP Exacer vs. followup (Severe Persistent) PLSDA M all 0.6489362
0.1386966 CTDSP2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0212766
1.7372205 CTSA Exacer vs. followup (Severe Persistent) PLSDA M all 0.9787234
1.3046308 CXCL10 Exacer vs. followup (Severe Persistent) PLSDA M all 0.8191489
0.7667622 CXCL2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.4148936
0.2328572 CXCL6 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0425532
1.2838530 DAP Exacer vs. followup (Severe Persistent) PLSDA M all 0.7978723
1.2708522 DESI1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.7659574
0.8802278 F13A1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.5000000
1.5105222 FAM8A1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.9255319
0.4971119 FOS Exacer vs. followup (Severe Persistent) PLSDA M all 0.2021277
0.6539989 FOXJ1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.2659574
0.9281356 FPR1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.5319149
0.7092497 FPR2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.3297872
0.4043475 FUT7 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0957447
0.4765746 GBE1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.1808511
1.2680730 GNAS Exacer vs. followup (Severe Persistent) PLSDA M all 0.7553191
0.4853963 GNLY Exacer vs. followup (Severe Persistent) PLSDA M all 0.1914894
1.2834166 IFI35 Exacer vs. followup (Severe Persistent) PLSDA M all 0.7872340
0.4604357 IFRD1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.1595745
0.5055353 IL15RA Exacer vs. followup (Severe Persistent) PLSDA M all 0.2234043
0.0348757 IL1R1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0000000
0.3009575 IL1R2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0638298
0.5381023 IL26 Exacer vs. followup (Severe Persistent) PLSDA M all 0.2340426
0.9312434 IL32 Exacer vs. followup (Severe Persistent) PLSDA M all 0.5425532
0.6775143 ITGA2B Exacer vs. followup (Severe Persistent) PLSDA M all 0.2872340
1.0657348 ITSN1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.6382979
0.4666038 JAM3 Exacer vs. followup (Severe Persistent) PLSDA M all 0.1702128
0.0823728 KIAA1551 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0106383
0.9421387 KRT23 Exacer vs. followup (Severe Persistent) PLSDA M all 0.5744681
0.7238471 LCN2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.3404255
0.7479778 LCP1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.3723404
1.7418101 LILRB1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.9893617
0.7593935 LMBRD1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.3936170
0.7361123 LYST Exacer vs. followup (Severe Persistent) PLSDA M all 0.3510638
1.4120753 MAP3K5 Exacer vs. followup (Severe Persistent) PLSDA M all 0.8829787
0.4451246 MAP3K8 Exacer vs. followup (Severe Persistent) PLSDA M all 0.1276596
0.6038825 MME Exacer vs. followup (Severe Persistent) PLSDA M all 0.2553191
1.3913620 MS4A2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.8723404
1.6152880 NAPA Exacer vs. followup (Severe Persistent) PLSDA M all 0.9574468
0.4568003 NFKBIA Exacer vs. followup (Severe Persistent) PLSDA M all 0.1489362
1.1076400 PABPC1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.6702128
0.8534011 PELI1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.4787234
0.4202558 PLAU Exacer vs. followup (Severe Persistent) PLSDA M all 0.1063830
0.7718249 PLXNC1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.4255319
0.8284946 PPBP Exacer vs. followup (Severe Persistent) PLSDA M all 0.4680851
0.7502207 PPP3R1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.3829787
0.9118929 PSEN1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.5212766
1.1349047 PTPN18 Exacer vs. followup (Severe Persistent) PLSDA M all 0.6914894
0.9398062 QKI Exacer vs. followup (Severe Persistent) PLSDA M all 0.5638298
0.7630066 RALGPS2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.4042553
0.8572447 RGS2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.4893617
1.2170012 SBNO2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.7234043
1.0613995 SELPLG Exacer vs. followup (Severe Persistent) PLSDA M all 0.6276596
0.4398813 SEMA4D Exacer vs. followup (Severe Persistent) PLSDA M all 0.1170213
1.2713613 SETX Exacer vs. followup (Severe Persistent) PLSDA M all 0.7765957
1.1529934 SF3B1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.7021277
1.3031287 SH2B2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.8085106
1.2603972 SH3BGRL3 Exacer vs. followup (Severe Persistent) PLSDA M all 0.7340426
0.9335869 SMCHD1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.5531915
0.5018163 SPINK5 Exacer vs. followup (Severe Persistent) PLSDA M all 0.2127660
0.8093874 SULT1A1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.4361702
1.5433500 TFEB Exacer vs. followup (Severe Persistent) PLSDA M all 0.9361702
1.6803851 TFRC Exacer vs. followup (Severe Persistent) PLSDA M all 0.9680851
0.5663461 TGFBI Exacer vs. followup (Severe Persistent) PLSDA M all 0.2446809
1.1216031 THY1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.6808511
0.8182276 TIA1 Exacer vs. followup (Severe Persistent) PLSDA M all 0.4468085
0.8246908 TLR7 Exacer vs. followup (Severe Persistent) PLSDA M all 0.4574468
0.7001777 TNFRSF10C Exacer vs. followup (Severe Persistent) PLSDA M all 0.3191489
0.8830002 TNFSF10 Exacer vs. followup (Severe Persistent) PLSDA M all 0.5106383
1.0561088 TNFSF4 Exacer vs. followup (Severe Persistent) PLSDA M all 0.6063830
0.3708068 ULBP2 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0851064
0.9890218 VCAN Exacer vs. followup (Severe Persistent) PLSDA M all 0.5851064
0.6784745 VPS13A Exacer vs. followup (Severe Persistent) PLSDA M all 0.2978723
1.1977665 ZNF185 Exacer vs. followup (Severe Persistent) PLSDA M all 0.7127660
0.2398762 ZNF281 Exacer vs. followup (Severe Persistent) PLSDA M all 0.0531915
1.0596474 ZNF609 Exacer vs. followup (Severe Persistent) PLSDA M all 0.6170213
1.6483319 NAPA Exacer vs. followup (Moderate Persistent) RF M UCSC 1.0000000
1.2215143 PABPC1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.9615385
1.1876886 FOS Exacer vs. followup (Moderate Persistent) RF M UCSC 0.9230769
1.1420024 SULT1A1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.8846154
0.9684946 CD8A Exacer vs. followup (Moderate Persistent) RF M UCSC 0.8461538
0.9632819 KRT23 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.8076923
0.7299384 GNLY Exacer vs. followup (Moderate Persistent) RF M UCSC 0.7692308
0.5030140 AHCTF1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.7307692
0.4978819 CASP8 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.6923077
0.4406599 CD4 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.6538462
0.4390029 ATP8A1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.6153846
0.4190581 DAP Exacer vs. followup (Moderate Persistent) RF M UCSC 0.5769231
0.3631776 CLEC4E Exacer vs. followup (Moderate Persistent) RF M UCSC 0.5384615
0.3573472 PPP3R1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.5000000
0.3440702 FAM8A1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.4615385
0.3433325 NFKBIA Exacer vs. followup (Moderate Persistent) RF M UCSC 0.4230769
0.3324228 C9orf78 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.3846154
0.2918336 SF3B1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.3461538
0.2891447 RGS2 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.3076923
0.2602302 LMBRD1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.2692308
0.2584685 CARM1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.2307692
0.2528424 FUT7 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.1923077
0.2317915 F13A1 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.1538462
0.2026021 SH3BGRL3 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.1153846
0.2005024 ABHD5 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.0769231
0.1731607 ZNF185 Exacer vs. followup (Moderate Persistent) RF M UCSC 0.0384615
0.1521904 TGFBI Exacer vs. followup (Moderate Persistent) RF M UCSC 0.0000000
3.5211971 NAPA Exacer vs. Quiet (Severe Persistent) RF M UCSC 1.0000000
1.9769944 GNLY Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.9615385
1.8468110 LMBRD1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.9230769
1.5826367 SF3B1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.8846154
1.4829411 ATP8A1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.8461538
1.2767308 CLEC4E Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.8076923
1.1282987 ZNF185 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.7692308
1.0385736 CD8A Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.7307692
0.9453193 KRT23 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.6923077
0.9406455 AHCTF1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.6538462
0.9033477 DAP Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.6153846
0.8604204 CARM1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.5769231
0.7525205 FAM8A1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.5384615
0.7463590 PABPC1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.5000000
0.7099340 ABHD5 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.4615385
0.7069263 SH3BGRL3 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.4230769
0.7028093 PPP3R1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.3846154
0.6923057 RGS2 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.3461538
0.6480655 FOS Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.3076923
0.5356884 C9orf78 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.2692308
0.5278921 TGFBI Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.2307692
0.5160690 F13A1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.1923077
0.4880163 SULT1A1 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.1538462
0.4851131 FUT7 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.1153846
0.4728528 CASP8 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.0769231
0.4359890 CD4 Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.0384615
0.3875606 NFKBIA Exacer vs. Quiet (Severe Persistent) RF M UCSC 0.0000000
3.8906030 COPB1 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 1.0000000
3.4947075 FPR2 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.9642857
3.2816135 GNLY Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.9285714
2.3721268 ZNF609 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.8928571
2.2789170 IL1R2 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.8571429
2.2266144 GNAS Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.8214286
2.0770466 SULT1A1 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.7857143
1.9809235 NAPA Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.7500000
1.8513830 TGFBI Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.7142857
1.8018028 NFKBIA Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.6785714
1.7775901 CLEC4E Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.6428571
1.7597839 PTPN18 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.6071429
1.7129056 MME Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.5714286
1.7030109 TIA1 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.5357143
1.5855105 VCAN Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.5000000
1.4432953 SH3BGRL3 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.4642857
1.4420080 SEMA4D Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.4285714
1.3167387 PLXNC1 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.3928571
1.3078328 F13A1 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.3571429
1.3053930 CD8A Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.3214286
1.2992624 ATP8A1 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.2857143
1.2519965 QKI Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.2500000
1.2159475 SF3B1 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.2142857
1.1934201 MAP3K8 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.1785714
1.1901156 FAM8A1 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.1428571
1.1798317 PELI1 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.1071429
1.1434725 RGS2 Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.0714286
1.1364117 VPS13A Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.0357143
1.0025358 ATP11A Exacer vs. followup (Moderate Persistent) RF M+F UCSC_isoforms 0.0000000
2.0359292 COPB1 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 1.0000000
1.5738640 FPR2 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.9642857
1.4393023 NAPA Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.9285714
0.9382633 SULT1A1 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.8928571
0.8308765 CD8A Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.8571429
0.7666487 PLXNC1 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.8214286
0.6238035 GNLY Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.7857143
0.4868828 CLEC4E Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.7500000
0.4420603 ATP8A1 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.7142857
0.4372391 PTPN18 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.6785714
0.3828086 QKI Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.6428571
0.3773260 ZNF609 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.6071429
0.3608587 FAM8A1 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.5714286
0.3443923 NFKBIA Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.5357143
0.3095928 SF3B1 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.5000000
0.2884452 IL1R2 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.4642857
0.2678763 GNAS Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.4285714
0.2485869 ATP11A Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.3928571
0.2458071 PELI1 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.3571429
0.2428644 RGS2 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.3214286
0.2283755 SEMA4D Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.2857143
0.2246229 F13A1 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.2500000
0.2217851 SH3BGRL3 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.2142857
0.2184514 VPS13A Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.1785714
0.2151287 TIA1 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.1428571
0.2113538 MME Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.1071429
0.1972939 VCAN Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.0714286
0.1783882 TGFBI Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.0357143
0.1420483 MAP3K8 Exacer vs. followup (Moderate Persistent) RF M UCSC_isoforms 0.0000000
1.4332446 CTSA Exacer vs. followup (Moderate Persistent) RF M Ensembl 1.0000000
1.2002262 PABPC1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.9642857
1.1928139 KRT23 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.9285714
0.8886618 CD8A Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.8928571
0.8736077 KIAA1551 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.8571429
0.7509738 GNLY Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.8214286
0.6599718 RALGPS2 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.7857143
0.5009654 AHCTF1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.7500000
0.4614926 ATP8A1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.7142857
0.4549311 DAP Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.6785714
0.4505017 CISH Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.6428571
0.4046119 SF3B1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.6071429
0.3930553 ZNF281 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.5714286
0.3873027 PPP3R1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.5357143
0.3827889 RGS2 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.5000000
0.3765292 SMCHD1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.4642857
0.3493112 C9orf78 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.4285714
0.3452193 FAM8A1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.3928571
0.3434742 DESI1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.3571429
0.3400410 CLEC4E Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.3214286
0.2579773 F13A1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.2857143
0.2518637 CHP1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.2500000
0.2478159 ITSN1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.2142857
0.2437364 CARM1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.1785714
0.1806314 ZNF185 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.1428571
0.1787140 TGFBI Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.1071429
0.1776296 SH3BGRL3 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.0714286
0.1724769 CTDSP2 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.0357143
0.1566044 GBE1 Exacer vs. followup (Moderate Persistent) RF M Ensembl 0.0000000
2.5434442 CTSA Exacer vs. Quiet (Severe Persistent) RF M Ensembl 1.0000000
2.0284684 GNLY Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.9642857
1.6398851 SF3B1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.9285714
1.5336018 ATP8A1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.8928571
1.4004773 ITSN1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.8571429
1.3558617 CLEC4E Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.8214286
1.2724168 CISH Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.7857143
0.9195698 CD8A Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.7500000
0.8646489 ZNF185 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.7142857
0.8567672 AHCTF1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.6785714
0.8557052 ZNF281 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.6428571
0.8523397 KRT23 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.6071429
0.7764252 DAP Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.5714286
0.7734722 KIAA1551 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.5357143
0.7438804 CARM1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.5000000
0.7129546 RALGPS2 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.4642857
0.7015388 DESI1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.4285714
0.6926284 PPP3R1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.3928571
0.6894176 PABPC1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.3571429
0.6547623 FAM8A1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.3214286
0.6393946 SH3BGRL3 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.2857143
0.5869285 SMCHD1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.2500000
0.5677264 RGS2 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.2142857
0.5174339 C9orf78 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.1785714
0.4930798 CTDSP2 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.1428571
0.4677419 F13A1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.1071429
0.4630648 TGFBI Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.0714286
0.3962731 CHP1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.0357143
0.3223546 GBE1 Exacer vs. Quiet (Severe Persistent) RF M Ensembl 0.0000000
2.9675732 CISH Exacer vs. followup (Severe Persistent) RF M Ensembl 1.0000000
1.4208627 C9orf78 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.9642857
1.2071977 CARM1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.9285714
0.8501989 FAM8A1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.8928571
0.7987276 CTSA Exacer vs. followup (Severe Persistent) RF M Ensembl 0.8571429
0.7806397 ATP8A1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.8214286
0.7575974 DAP Exacer vs. followup (Severe Persistent) RF M Ensembl 0.7857143
0.5618383 SF3B1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.7500000
0.5566718 ITSN1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.7142857
0.5405840 CHP1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.6785714
0.5380819 CLEC4E Exacer vs. followup (Severe Persistent) RF M Ensembl 0.6428571
0.5307837 CD8A Exacer vs. followup (Severe Persistent) RF M Ensembl 0.6071429
0.4996230 PPP3R1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.5714286
0.4860007 GNLY Exacer vs. followup (Severe Persistent) RF M Ensembl 0.5357143
0.4743808 TGFBI Exacer vs. followup (Severe Persistent) RF M Ensembl 0.5000000
0.4171533 KRT23 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.4642857
0.3538965 SMCHD1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.4285714
0.3461305 KIAA1551 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.3928571
0.3254522 SH3BGRL3 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.3571429
0.3239945 RALGPS2 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.3214286
0.2994798 DESI1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.2857143
0.2834036 AHCTF1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.2500000
0.2703298 RGS2 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.2142857
0.2533589 ZNF281 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.1785714
0.2471389 CTDSP2 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.1428571
0.2451860 PABPC1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.1071429
0.2227164 GBE1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.0714286
0.2071250 ZNF185 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.0357143
0.1971144 F13A1 Exacer vs. followup (Severe Persistent) RF M Ensembl 0.0000000
2.9792244 FPR2 Exacer vs. followup (Moderate Persistent) RF M Trinity 1.0000000
2.5830493 CECR1 Exacer vs. followup (Moderate Persistent) RF M Trinity 0.8888889
2.0992622 LYST Exacer vs. followup (Moderate Persistent) RF M Trinity 0.7777778
1.5831344 FPR1 Exacer vs. followup (Moderate Persistent) RF M Trinity 0.6666667
1.1912095 SETX Exacer vs. followup (Moderate Persistent) RF M Trinity 0.5555556
1.0114469 QKI Exacer vs. followup (Moderate Persistent) RF M Trinity 0.4444444
0.8956291 CASP8 Exacer vs. followup (Moderate Persistent) RF M Trinity 0.3333333
0.6256590 IFRD1 Exacer vs. followup (Moderate Persistent) RF M Trinity 0.2222222
0.5673338 TNFRSF10C Exacer vs. followup (Moderate Persistent) RF M Trinity 0.1111111
0.5452258 SF3B1 Exacer vs. followup (Moderate Persistent) RF M Trinity 0.0000000
4.6763890 IFI35 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 1.0000000
3.0343676 IL32 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.9729730
2.9012682 TFRC Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.9459459
2.7436535 LCP1 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.9189189
2.7233895 TNFSF10 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.8918919
1.7324530 SELPLG Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.8648649
1.5690020 IL1R1 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.8378378
1.5678528 FOXJ1 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.8108108
1.5241533 JAM3 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.7837838
1.4176183 F13A1 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.7567568
1.3071295 CDH1 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.7297297
1.2874249 CD55 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.7027027
1.2444854 SPINK5 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.6756757
1.2334565 CXCL2 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.6486486
1.2206217 MS4A2 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.6216216
1.2197747 TNFSF4 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.5945946
1.2140558 LCN2 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.5675676
1.1783080 MAP3K5 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.5405405
1.1432048 ULBP2 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.5135135
1.1402292 PSEN1 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.4864865
1.1343725 FUT7 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.4594595
1.1073369 ITGA2B Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.4324324
1.0360764 SH2B2 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.4054054
1.0079184 CXCL6 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.3783784
0.9811892 CREBBP Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.3513514
0.9769498 LILRB1 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.3243243
0.9679311 PPBP Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.2972973
0.9353799 CXCL10 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.2702703
0.9196267 IL26 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.2432432
0.9125187 FOS Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.2162162
0.8610929 SBNO2 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.1891892
0.8031919 THY1 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.1621622
0.7916470 TLR7 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.1351351
0.7816229 CD48 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.1081081
0.7374204 PLAU Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.0810811
0.7320900 TFEB Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.0540541
0.6529100 ARG2 Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.0270270
0.6363121 IL15RA Exacer vs. followup (Moderate Persistent) RF M+F panCancer 0.0000000
5.1761319 LCN2 Exacer vs. followup (Severe Persistent) RF M+F panCancer 1.0000000
3.1767779 SBNO2 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.9729730
3.1635956 TFRC Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.9459459
3.1211546 LILRB1 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.9189189
2.5560346 ARG2 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.8918919
2.4590297 TLR7 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.8648649
1.7287213 CXCL10 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.8378378
1.6487809 FOXJ1 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.8108108
1.5450024 THY1 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.7837838
1.4698245 PPBP Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.7567568
1.3898354 CREBBP Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.7297297
1.3317471 FOS Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.7027027
1.3175328 F13A1 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.6756757
1.3073323 IL1R1 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.6486486
1.2907947 SH2B2 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.6216216
1.2014450 SPINK5 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.5945946
1.1888926 TNFSF4 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.5675676
1.1878343 LCP1 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.5405405
1.1836741 FUT7 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.5135135
1.1732938 MAP3K5 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.4864865
1.0951154 CD48 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.4594595
1.0544187 TNFSF10 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.4324324
1.0348299 IL32 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.4054054
1.0119744 IFI35 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.3783784
1.0054395 ULBP2 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.3513514
0.9860552 PLAU Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.3243243
0.9623855 CXCL2 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.2972973
0.9348970 CXCL6 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.2702703
0.9028410 SELPLG Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.2432432
0.8910652 CD55 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.2162162
0.8892866 CDH1 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.1891892
0.8851047 IL15RA Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.1621622
0.8754585 ITGA2B Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.1351351
0.8650684 IL26 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.1081081
0.8599673 TFEB Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.0810811
0.8467405 JAM3 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.0540541
0.8118223 PSEN1 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.0270270
0.7930909 MS4A2 Exacer vs. followup (Severe Persistent) RF M+F panCancer 0.0000000
1.5064110 LCP1 Exacer vs. followup (Moderate Persistent) RF M panCancer 1.0000000
1.3571805 IFI35 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.9729730
0.8552221 SH2B2 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.9459459
0.8366085 SELPLG Exacer vs. followup (Moderate Persistent) RF M panCancer 0.9189189
0.8256620 TFEB Exacer vs. followup (Moderate Persistent) RF M panCancer 0.8918919
0.7764311 FOS Exacer vs. followup (Moderate Persistent) RF M panCancer 0.8648649
0.7353732 IL26 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.8378378
0.6805554 CXCL10 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.8108108
0.6612078 SPINK5 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.7837838
0.5576226 PSEN1 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.7567568
0.4872952 CXCL6 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.7297297
0.3832219 CXCL2 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.7027027
0.3576760 LILRB1 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.6756757
0.3367590 PPBP Exacer vs. followup (Moderate Persistent) RF M panCancer 0.6486486
0.3259764 CDH1 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.6216216
0.2869146 MS4A2 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.5945946
0.2632695 TNFSF10 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.5675676
0.2530777 IL32 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.5405405
0.2398407 THY1 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.5135135
0.2257727 JAM3 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.4864865
0.2210258 CD48 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.4594595
0.2118259 TLR7 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.4324324
0.2027532 MAP3K5 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.4054054
0.1711214 F13A1 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.3783784
0.1587560 ARG2 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.3513514
0.1585486 FOXJ1 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.3243243
0.1578662 IL15RA Exacer vs. followup (Moderate Persistent) RF M panCancer 0.2972973
0.1564844 CD55 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.2702703
0.1395892 FUT7 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.2432432
0.1382282 TFRC Exacer vs. followup (Moderate Persistent) RF M panCancer 0.2162162
0.1332447 CREBBP Exacer vs. followup (Moderate Persistent) RF M panCancer 0.1891892
0.1320836 ITGA2B Exacer vs. followup (Moderate Persistent) RF M panCancer 0.1621622
0.1300441 IL1R1 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.1351351
0.1267262 SBNO2 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.1081081
0.1177810 ULBP2 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.0810811
0.1166618 PLAU Exacer vs. followup (Moderate Persistent) RF M panCancer 0.0540541
0.0982033 LCN2 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.0270270
0.0924459 TNFSF4 Exacer vs. followup (Moderate Persistent) RF M panCancer 0.0000000
2.4992493 IFI35 Exacer vs. followup (Moderate Persistent) RF M+F all 1.0000000
1.5590806 COPB1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.9893617
1.5321412 TFRC Exacer vs. followup (Moderate Persistent) RF M+F all 0.9787234
1.5313017 TNFSF10 Exacer vs. followup (Moderate Persistent) RF M+F all 0.9680851
1.5192547 CTDSP2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.9574468
1.4282795 IL32 Exacer vs. followup (Moderate Persistent) RF M+F all 0.9468085
1.4018036 CECR1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.9361702
1.2705644 FPR2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.9255319
1.2496324 LCP1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.9148936
1.2092522 GNLY Exacer vs. followup (Moderate Persistent) RF M+F all 0.9042553
1.0925521 PPP3R1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.8936170
0.9585687 CTSA Exacer vs. followup (Moderate Persistent) RF M+F all 0.8829787
0.8115574 SULT1A1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.8723404
0.7841895 FOXJ1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.8617021
0.7657442 RALGPS2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.8510638
0.7204773 SELPLG Exacer vs. followup (Moderate Persistent) RF M+F all 0.8404255
0.7176659 ZNF609 Exacer vs. followup (Moderate Persistent) RF M+F all 0.8297872
0.6892771 JAM3 Exacer vs. followup (Moderate Persistent) RF M+F all 0.8191489
0.6732067 TGFBI Exacer vs. followup (Moderate Persistent) RF M+F all 0.8085106
0.6247116 FPR1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.7978723
0.5984826 VCAN Exacer vs. followup (Moderate Persistent) RF M+F all 0.7872340
0.5894501 PABPC1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.7765957
0.5868274 IL1R2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.7659574
0.5721608 IL1R1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.7553191
0.5693180 LCN2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.7446809
0.5640821 CARM1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.7340426
0.5608685 LYST Exacer vs. followup (Moderate Persistent) RF M+F all 0.7234043
0.5513177 MS4A2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.7127660
0.5481626 NAPA Exacer vs. followup (Moderate Persistent) RF M+F all 0.7021277
0.5435996 TNFSF4 Exacer vs. followup (Moderate Persistent) RF M+F all 0.6914894
0.5394723 SEMA4D Exacer vs. followup (Moderate Persistent) RF M+F all 0.6808511
0.5366075 CD55 Exacer vs. followup (Moderate Persistent) RF M+F all 0.6702128
0.5304477 PTPN18 Exacer vs. followup (Moderate Persistent) RF M+F all 0.6595745
0.5303258 CDH1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.6489362
0.5237753 GNAS Exacer vs. followup (Moderate Persistent) RF M+F all 0.6382979
0.5223673 FUT7 Exacer vs. followup (Moderate Persistent) RF M+F all 0.6276596
0.5208003 GBE1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.6170213
0.5207901 CLEC4E Exacer vs. followup (Moderate Persistent) RF M+F all 0.6063830
0.5093770 TIA1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.5957447
0.5012580 SPINK5 Exacer vs. followup (Moderate Persistent) RF M+F all 0.5851064
0.4994948 PSEN1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.5744681
0.4972576 ULBP2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.5638298
0.4809378 MME Exacer vs. followup (Moderate Persistent) RF M+F all 0.5531915
0.4587081 NFKBIA Exacer vs. followup (Moderate Persistent) RF M+F all 0.5425532
0.4556900 CD4 Exacer vs. followup (Moderate Persistent) RF M+F all 0.5319149
0.4477971 CXCL2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.5212766
0.4450328 CASP8 Exacer vs. followup (Moderate Persistent) RF M+F all 0.5106383
0.4445303 MAP3K5 Exacer vs. followup (Moderate Persistent) RF M+F all 0.5000000
0.4395425 F13A1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.4893617
0.4216989 SF3B1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.4787234
0.4057397 C9orf78 Exacer vs. followup (Moderate Persistent) RF M+F all 0.4680851
0.4036545 CD8A Exacer vs. followup (Moderate Persistent) RF M+F all 0.4574468
0.4023768 KRT23 Exacer vs. followup (Moderate Persistent) RF M+F all 0.4468085
0.4002584 IFRD1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.4361702
0.3896357 FOS Exacer vs. followup (Moderate Persistent) RF M+F all 0.4255319
0.3825598 QKI Exacer vs. followup (Moderate Persistent) RF M+F all 0.4148936
0.3824130 SH2B2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.4042553
0.3749221 PPBP Exacer vs. followup (Moderate Persistent) RF M+F all 0.3936170
0.3710450 CISH Exacer vs. followup (Moderate Persistent) RF M+F all 0.3829787
0.3653304 CXCL10 Exacer vs. followup (Moderate Persistent) RF M+F all 0.3723404
0.3649257 LMBRD1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.3617021
0.3580858 SH3BGRL3 Exacer vs. followup (Moderate Persistent) RF M+F all 0.3510638
0.3531470 CXCL6 Exacer vs. followup (Moderate Persistent) RF M+F all 0.3404255
0.3464034 PLXNC1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.3297872
0.3450587 RGS2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.3191489
0.3429578 ATP8A1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.3085106
0.3423992 CD48 Exacer vs. followup (Moderate Persistent) RF M+F all 0.2978723
0.3422331 CREBBP Exacer vs. followup (Moderate Persistent) RF M+F all 0.2872340
0.3390372 ZNF281 Exacer vs. followup (Moderate Persistent) RF M+F all 0.2765957
0.3388144 IL26 Exacer vs. followup (Moderate Persistent) RF M+F all 0.2659574
0.3379404 ITGA2B Exacer vs. followup (Moderate Persistent) RF M+F all 0.2553191
0.3314107 KIAA1551 Exacer vs. followup (Moderate Persistent) RF M+F all 0.2446809
0.3293782 ITSN1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.2340426
0.3273829 THY1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.2234043
0.3241534 CHP1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.2127660
0.3181441 LILRB1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.2021277
0.3180674 VPS13A Exacer vs. followup (Moderate Persistent) RF M+F all 0.1914894
0.3167278 PELI1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.1808511
0.3148383 TNFRSF10C Exacer vs. followup (Moderate Persistent) RF M+F all 0.1702128
0.3139736 AHCTF1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.1595745
0.3114090 SMCHD1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.1489362
0.3109895 ABHD5 Exacer vs. followup (Moderate Persistent) RF M+F all 0.1382979
0.3071238 MAP3K8 Exacer vs. followup (Moderate Persistent) RF M+F all 0.1276596
0.3060691 SETX Exacer vs. followup (Moderate Persistent) RF M+F all 0.1170213
0.3055129 DAP Exacer vs. followup (Moderate Persistent) RF M+F all 0.1063830
0.3043818 SBNO2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.0957447
0.3007054 TLR7 Exacer vs. followup (Moderate Persistent) RF M+F all 0.0851064
0.2994434 FAM8A1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.0744681
0.2989667 ZNF185 Exacer vs. followup (Moderate Persistent) RF M+F all 0.0638298
0.2985182 PLAU Exacer vs. followup (Moderate Persistent) RF M+F all 0.0531915
0.2773992 IL15RA Exacer vs. followup (Moderate Persistent) RF M+F all 0.0425532
0.2701149 DESI1 Exacer vs. followup (Moderate Persistent) RF M+F all 0.0319149
0.2532216 TFEB Exacer vs. followup (Moderate Persistent) RF M+F all 0.0212766
0.2477506 ATP11A Exacer vs. followup (Moderate Persistent) RF M+F all 0.0106383
0.2332065 ARG2 Exacer vs. followup (Moderate Persistent) RF M+F all 0.0000000
0.8432418 COPB1 Exacer vs. followup (Moderate Persistent) RF M all 1.0000000
0.6806352 LCP1 Exacer vs. followup (Moderate Persistent) RF M all 0.9893617
0.6618034 IFI35 Exacer vs. followup (Moderate Persistent) RF M all 0.9787234
0.5983545 FPR2 Exacer vs. followup (Moderate Persistent) RF M all 0.9680851
0.5152984 NAPA Exacer vs. followup (Moderate Persistent) RF M all 0.9574468
0.4409555 CTSA Exacer vs. followup (Moderate Persistent) RF M all 0.9468085
0.4404084 SH2B2 Exacer vs. followup (Moderate Persistent) RF M all 0.9361702
0.4028379 SELPLG Exacer vs. followup (Moderate Persistent) RF M all 0.9255319
0.3907419 CECR1 Exacer vs. followup (Moderate Persistent) RF M all 0.9148936
0.3687625 TFEB Exacer vs. followup (Moderate Persistent) RF M all 0.9042553
0.3508908 CXCL10 Exacer vs. followup (Moderate Persistent) RF M all 0.8936170
0.3437976 PABPC1 Exacer vs. followup (Moderate Persistent) RF M all 0.8829787
0.3322482 FOS Exacer vs. followup (Moderate Persistent) RF M all 0.8723404
0.3222834 LYST Exacer vs. followup (Moderate Persistent) RF M all 0.8617021
0.3146154 IL26 Exacer vs. followup (Moderate Persistent) RF M all 0.8510638
0.3082532 SPINK5 Exacer vs. followup (Moderate Persistent) RF M all 0.8404255
0.3014327 CD8A Exacer vs. followup (Moderate Persistent) RF M all 0.8297872
0.2836917 SULT1A1 Exacer vs. followup (Moderate Persistent) RF M all 0.8191489
0.2714251 KRT23 Exacer vs. followup (Moderate Persistent) RF M all 0.8085106
0.2683609 PLXNC1 Exacer vs. followup (Moderate Persistent) RF M all 0.7978723
0.2581258 KIAA1551 Exacer vs. followup (Moderate Persistent) RF M all 0.7872340
0.2511248 PSEN1 Exacer vs. followup (Moderate Persistent) RF M all 0.7765957
0.2120294 CXCL6 Exacer vs. followup (Moderate Persistent) RF M all 0.7659574
0.2043998 FPR1 Exacer vs. followup (Moderate Persistent) RF M all 0.7553191
0.1994261 SETX Exacer vs. followup (Moderate Persistent) RF M all 0.7446809
0.1749906 GNLY Exacer vs. followup (Moderate Persistent) RF M all 0.7340426
0.1680009 RALGPS2 Exacer vs. followup (Moderate Persistent) RF M all 0.7234043
0.1554087 LILRB1 Exacer vs. followup (Moderate Persistent) RF M all 0.7127660
0.1547540 CDH1 Exacer vs. followup (Moderate Persistent) RF M all 0.7021277
0.1479730 PPBP Exacer vs. followup (Moderate Persistent) RF M all 0.6914894
0.1465464 CXCL2 Exacer vs. followup (Moderate Persistent) RF M all 0.6808511
0.1325185 AHCTF1 Exacer vs. followup (Moderate Persistent) RF M all 0.6702128
0.1307489 CD4 Exacer vs. followup (Moderate Persistent) RF M all 0.6595745
0.1243429 PTPN18 Exacer vs. followup (Moderate Persistent) RF M all 0.6489362
0.1217411 CASP8 Exacer vs. followup (Moderate Persistent) RF M all 0.6382979
0.1141595 CLEC4E Exacer vs. followup (Moderate Persistent) RF M all 0.6276596
0.1132913 QKI Exacer vs. followup (Moderate Persistent) RF M all 0.6170213
0.1120503 IL32 Exacer vs. followup (Moderate Persistent) RF M all 0.6063830
0.1092749 CISH Exacer vs. followup (Moderate Persistent) RF M all 0.5957447
0.1086943 ZNF281 Exacer vs. followup (Moderate Persistent) RF M all 0.5851064
0.1070915 TNFSF10 Exacer vs. followup (Moderate Persistent) RF M all 0.5744681
0.1058054 MS4A2 Exacer vs. followup (Moderate Persistent) RF M all 0.5638298
0.1044493 ATP8A1 Exacer vs. followup (Moderate Persistent) RF M all 0.5531915
0.0996354 RGS2 Exacer vs. followup (Moderate Persistent) RF M all 0.5425532
0.0958575 ZNF609 Exacer vs. followup (Moderate Persistent) RF M all 0.5319149
0.0929231 PPP3R1 Exacer vs. followup (Moderate Persistent) RF M all 0.5212766
0.0920698 CD48 Exacer vs. followup (Moderate Persistent) RF M all 0.5106383
0.0905601 THY1 Exacer vs. followup (Moderate Persistent) RF M all 0.5000000
0.0904015 DAP Exacer vs. followup (Moderate Persistent) RF M all 0.4893617
0.0866161 TNFRSF10C Exacer vs. followup (Moderate Persistent) RF M all 0.4787234
0.0850706 NFKBIA Exacer vs. followup (Moderate Persistent) RF M all 0.4680851
0.0842794 IFRD1 Exacer vs. followup (Moderate Persistent) RF M all 0.4574468
0.0824751 JAM3 Exacer vs. followup (Moderate Persistent) RF M all 0.4468085
0.0810823 TLR7 Exacer vs. followup (Moderate Persistent) RF M all 0.4361702
0.0802064 FAM8A1 Exacer vs. followup (Moderate Persistent) RF M all 0.4255319
0.0796094 SF3B1 Exacer vs. followup (Moderate Persistent) RF M all 0.4148936
0.0744203 MAP3K5 Exacer vs. followup (Moderate Persistent) RF M all 0.4042553
0.0706146 IL1R1 Exacer vs. followup (Moderate Persistent) RF M all 0.3936170
0.0682518 ITSN1 Exacer vs. followup (Moderate Persistent) RF M all 0.3829787
0.0678172 SMCHD1 Exacer vs. followup (Moderate Persistent) RF M all 0.3723404
0.0657266 DESI1 Exacer vs. followup (Moderate Persistent) RF M all 0.3617021
0.0653213 TFRC Exacer vs. followup (Moderate Persistent) RF M all 0.3510638
0.0648434 VPS13A Exacer vs. followup (Moderate Persistent) RF M all 0.3404255
0.0647311 ARG2 Exacer vs. followup (Moderate Persistent) RF M all 0.3297872
0.0644586 SEMA4D Exacer vs. followup (Moderate Persistent) RF M all 0.3191489
0.0624633 IL15RA Exacer vs. followup (Moderate Persistent) RF M all 0.3085106
0.0624112 IL1R2 Exacer vs. followup (Moderate Persistent) RF M all 0.2978723
0.0596049 GNAS Exacer vs. followup (Moderate Persistent) RF M all 0.2872340
0.0559308 CD55 Exacer vs. followup (Moderate Persistent) RF M all 0.2765957
0.0557631 FOXJ1 Exacer vs. followup (Moderate Persistent) RF M all 0.2659574
0.0557504 ULBP2 Exacer vs. followup (Moderate Persistent) RF M all 0.2553191
0.0552915 C9orf78 Exacer vs. followup (Moderate Persistent) RF M all 0.2446809
0.0542578 TIA1 Exacer vs. followup (Moderate Persistent) RF M all 0.2340426
0.0536453 F13A1 Exacer vs. followup (Moderate Persistent) RF M all 0.2234043
0.0534446 FUT7 Exacer vs. followup (Moderate Persistent) RF M all 0.2127660
0.0531091 ATP11A Exacer vs. followup (Moderate Persistent) RF M all 0.2021277
0.0528648 CARM1 Exacer vs. followup (Moderate Persistent) RF M all 0.1914894
0.0526577 MME Exacer vs. followup (Moderate Persistent) RF M all 0.1808511
0.0526434 CHP1 Exacer vs. followup (Moderate Persistent) RF M all 0.1702128
0.0490216 SH3BGRL3 Exacer vs. followup (Moderate Persistent) RF M all 0.1595745
0.0489080 ABHD5 Exacer vs. followup (Moderate Persistent) RF M all 0.1489362
0.0483535 PELI1 Exacer vs. followup (Moderate Persistent) RF M all 0.1382979
0.0476859 LMBRD1 Exacer vs. followup (Moderate Persistent) RF M all 0.1276596
0.0439287 VCAN Exacer vs. followup (Moderate Persistent) RF M all 0.1170213
0.0435539 CREBBP Exacer vs. followup (Moderate Persistent) RF M all 0.1063830
0.0433843 ITGA2B Exacer vs. followup (Moderate Persistent) RF M all 0.0957447
0.0430531 TGFBI Exacer vs. followup (Moderate Persistent) RF M all 0.0851064
0.0427473 MAP3K8 Exacer vs. followup (Moderate Persistent) RF M all 0.0744681
0.0426412 ZNF185 Exacer vs. followup (Moderate Persistent) RF M all 0.0638298
0.0407514 GBE1 Exacer vs. followup (Moderate Persistent) RF M all 0.0531915
0.0389356 SBNO2 Exacer vs. followup (Moderate Persistent) RF M all 0.0425532
0.0349038 TNFSF4 Exacer vs. followup (Moderate Persistent) RF M all 0.0319149
0.0335562 LCN2 Exacer vs. followup (Moderate Persistent) RF M all 0.0212766
0.0326096 CTDSP2 Exacer vs. followup (Moderate Persistent) RF M all 0.0106383
0.0289418 PLAU Exacer vs. followup (Moderate Persistent) RF M all 0.0000000
1.5995743 NAPA Exacer vs. Quiet (Severe Persistent) RF M all 1.0000000
1.0660948 CTSA Exacer vs. Quiet (Severe Persistent) RF M all 0.9893617
0.7149678 PLAU Exacer vs. Quiet (Severe Persistent) RF M all 0.9787234
0.7006343 LILRB1 Exacer vs. Quiet (Severe Persistent) RF M all 0.9680851
0.6754472 GNLY Exacer vs. Quiet (Severe Persistent) RF M all 0.9574468
0.6545321 LMBRD1 Exacer vs. Quiet (Severe Persistent) RF M all 0.9468085
0.6226345 CD55 Exacer vs. Quiet (Severe Persistent) RF M all 0.9361702
0.5978595 TNFSF10 Exacer vs. Quiet (Severe Persistent) RF M all 0.9255319
0.5902124 ARG2 Exacer vs. Quiet (Severe Persistent) RF M all 0.9148936
0.5683082 SBNO2 Exacer vs. Quiet (Severe Persistent) RF M all 0.9042553
0.5590501 SF3B1 Exacer vs. Quiet (Severe Persistent) RF M all 0.8936170
0.5567732 ITSN1 Exacer vs. Quiet (Severe Persistent) RF M all 0.8829787
0.5517946 CLEC4E Exacer vs. Quiet (Severe Persistent) RF M all 0.8723404
0.5270537 IFI35 Exacer vs. Quiet (Severe Persistent) RF M all 0.8617021
0.5224446 ATP8A1 Exacer vs. Quiet (Severe Persistent) RF M all 0.8510638
0.5010799 CREBBP Exacer vs. Quiet (Severe Persistent) RF M all 0.8404255
0.4635815 TFRC Exacer vs. Quiet (Severe Persistent) RF M all 0.8297872
0.4313360 CXCL10 Exacer vs. Quiet (Severe Persistent) RF M all 0.8191489
0.4262272 CISH Exacer vs. Quiet (Severe Persistent) RF M all 0.8085106
0.4112705 CD48 Exacer vs. Quiet (Severe Persistent) RF M all 0.7978723
0.4005557 TFEB Exacer vs. Quiet (Severe Persistent) RF M all 0.7872340
0.3888777 TNFRSF10C Exacer vs. Quiet (Severe Persistent) RF M all 0.7765957
0.3818647 ZNF185 Exacer vs. Quiet (Severe Persistent) RF M all 0.7659574
0.3601640 IL1R1 Exacer vs. Quiet (Severe Persistent) RF M all 0.7553191
0.3093180 TLR7 Exacer vs. Quiet (Severe Persistent) RF M all 0.7446809
0.3065468 CD8A Exacer vs. Quiet (Severe Persistent) RF M all 0.7340426
0.3049673 ZNF281 Exacer vs. Quiet (Severe Persistent) RF M all 0.7234043
0.2973143 KIAA1551 Exacer vs. Quiet (Severe Persistent) RF M all 0.7127660
0.2893135 LCP1 Exacer vs. Quiet (Severe Persistent) RF M all 0.7021277
0.2791582 DAP Exacer vs. Quiet (Severe Persistent) RF M all 0.6914894
0.2788271 LCN2 Exacer vs. Quiet (Severe Persistent) RF M all 0.6808511
0.2685365 KRT23 Exacer vs. Quiet (Severe Persistent) RF M all 0.6702128
0.2637961 FOXJ1 Exacer vs. Quiet (Severe Persistent) RF M all 0.6595745
0.2633822 IL1R2 Exacer vs. Quiet (Severe Persistent) RF M all 0.6489362
0.2561331 DESI1 Exacer vs. Quiet (Severe Persistent) RF M all 0.6382979
0.2554552 FAM8A1 Exacer vs. Quiet (Severe Persistent) RF M all 0.6276596
0.2519666 QKI Exacer vs. Quiet (Severe Persistent) RF M all 0.6170213
0.2515763 FPR2 Exacer vs. Quiet (Severe Persistent) RF M all 0.6063830
0.2458430 ATP11A Exacer vs. Quiet (Severe Persistent) RF M all 0.5957447
0.2442738 CARM1 Exacer vs. Quiet (Severe Persistent) RF M all 0.5851064
0.2367909 SPINK5 Exacer vs. Quiet (Severe Persistent) RF M all 0.5744681
0.2355991 TIA1 Exacer vs. Quiet (Severe Persistent) RF M all 0.5638298
0.2304390 PPP3R1 Exacer vs. Quiet (Severe Persistent) RF M all 0.5531915
0.2302586 CECR1 Exacer vs. Quiet (Severe Persistent) RF M all 0.5425532
0.2170319 RGS2 Exacer vs. Quiet (Severe Persistent) RF M all 0.5319149
0.2168446 GNAS Exacer vs. Quiet (Severe Persistent) RF M all 0.5212766
0.2161923 AHCTF1 Exacer vs. Quiet (Severe Persistent) RF M all 0.5106383
0.2139182 PABPC1 Exacer vs. Quiet (Severe Persistent) RF M all 0.5000000
0.2136967 RALGPS2 Exacer vs. Quiet (Severe Persistent) RF M all 0.4893617
0.2131007 SH3BGRL3 Exacer vs. Quiet (Severe Persistent) RF M all 0.4787234
0.2042368 SH2B2 Exacer vs. Quiet (Severe Persistent) RF M all 0.4680851
0.1996121 TNFSF4 Exacer vs. Quiet (Severe Persistent) RF M all 0.4574468
0.1985879 IFRD1 Exacer vs. Quiet (Severe Persistent) RF M all 0.4468085
0.1888790 VCAN Exacer vs. Quiet (Severe Persistent) RF M all 0.4361702
0.1871448 IL26 Exacer vs. Quiet (Severe Persistent) RF M all 0.4255319
0.1866361 FOS Exacer vs. Quiet (Severe Persistent) RF M all 0.4148936
0.1826209 MME Exacer vs. Quiet (Severe Persistent) RF M all 0.4042553
0.1798010 ABHD5 Exacer vs. Quiet (Severe Persistent) RF M all 0.3936170
0.1775425 THY1 Exacer vs. Quiet (Severe Persistent) RF M all 0.3829787
0.1758190 MS4A2 Exacer vs. Quiet (Severe Persistent) RF M all 0.3723404
0.1705299 FPR1 Exacer vs. Quiet (Severe Persistent) RF M all 0.3617021
0.1656096 ITGA2B Exacer vs. Quiet (Severe Persistent) RF M all 0.3510638
0.1649987 SMCHD1 Exacer vs. Quiet (Severe Persistent) RF M all 0.3404255
0.1646773 MAP3K8 Exacer vs. Quiet (Severe Persistent) RF M all 0.3297872
0.1578163 SETX Exacer vs. Quiet (Severe Persistent) RF M all 0.3191489
0.1559633 SELPLG Exacer vs. Quiet (Severe Persistent) RF M all 0.3085106
0.1542973 PPBP Exacer vs. Quiet (Severe Persistent) RF M all 0.2978723
0.1460887 F13A1 Exacer vs. Quiet (Severe Persistent) RF M all 0.2872340
0.1431690 PSEN1 Exacer vs. Quiet (Severe Persistent) RF M all 0.2765957
0.1381847 CDH1 Exacer vs. Quiet (Severe Persistent) RF M all 0.2659574
0.1331874 CTDSP2 Exacer vs. Quiet (Severe Persistent) RF M all 0.2553191
0.1324199 JAM3 Exacer vs. Quiet (Severe Persistent) RF M all 0.2446809
0.1309536 CASP8 Exacer vs. Quiet (Severe Persistent) RF M all 0.2340426
0.1277235 C9orf78 Exacer vs. Quiet (Severe Persistent) RF M all 0.2234043
0.1268394 VPS13A Exacer vs. Quiet (Severe Persistent) RF M all 0.2127660
0.1263002 PLXNC1 Exacer vs. Quiet (Severe Persistent) RF M all 0.2021277
0.1251611 FUT7 Exacer vs. Quiet (Severe Persistent) RF M all 0.1914894
0.1251352 IL15RA Exacer vs. Quiet (Severe Persistent) RF M all 0.1808511
0.1219146 CXCL2 Exacer vs. Quiet (Severe Persistent) RF M all 0.1702128
0.1204470 PTPN18 Exacer vs. Quiet (Severe Persistent) RF M all 0.1595745
0.1190565 MAP3K5 Exacer vs. Quiet (Severe Persistent) RF M all 0.1489362
0.1183569 CXCL6 Exacer vs. Quiet (Severe Persistent) RF M all 0.1382979
0.1176376 COPB1 Exacer vs. Quiet (Severe Persistent) RF M all 0.1276596
0.1143271 SEMA4D Exacer vs. Quiet (Severe Persistent) RF M all 0.1170213
0.1128748 CHP1 Exacer vs. Quiet (Severe Persistent) RF M all 0.1063830
0.1125037 ULBP2 Exacer vs. Quiet (Severe Persistent) RF M all 0.0957447
0.1115709 TGFBI Exacer vs. Quiet (Severe Persistent) RF M all 0.0851064
0.1112852 SULT1A1 Exacer vs. Quiet (Severe Persistent) RF M all 0.0744681
0.1105531 PELI1 Exacer vs. Quiet (Severe Persistent) RF M all 0.0638298
0.1094487 ZNF609 Exacer vs. Quiet (Severe Persistent) RF M all 0.0531915
0.1030929 LYST Exacer vs. Quiet (Severe Persistent) RF M all 0.0425532
0.1010073 CD4 Exacer vs. Quiet (Severe Persistent) RF M all 0.0319149
0.0990358 IL32 Exacer vs. Quiet (Severe Persistent) RF M all 0.0212766
0.0974917 GBE1 Exacer vs. Quiet (Severe Persistent) RF M all 0.0106383
0.0940564 NFKBIA Exacer vs. Quiet (Severe Persistent) RF M all 0.0000000
1.4034011 CISH Exacer vs. followup (Severe Persistent) RF M all 1.0000000
0.9060675 LILRB1 Exacer vs. followup (Severe Persistent) RF M all 0.9893617
0.6747551 NAPA Exacer vs. followup (Severe Persistent) RF M all 0.9787234
0.5399177 C9orf78 Exacer vs. followup (Severe Persistent) RF M all 0.9680851
0.4784575 CD48 Exacer vs. followup (Severe Persistent) RF M all 0.9574468
0.4463557 CARM1 Exacer vs. followup (Severe Persistent) RF M all 0.9468085
0.3990510 TFRC Exacer vs. followup (Severe Persistent) RF M all 0.9361702
0.3870766 TNFRSF10C Exacer vs. followup (Severe Persistent) RF M all 0.9255319
0.3584940 SETX Exacer vs. followup (Severe Persistent) RF M all 0.9148936
0.3526188 SBNO2 Exacer vs. followup (Severe Persistent) RF M all 0.9042553
0.3468955 CECR1 Exacer vs. followup (Severe Persistent) RF M all 0.8936170
0.3404579 ARG2 Exacer vs. followup (Severe Persistent) RF M all 0.8829787
0.3359806 FAM8A1 Exacer vs. followup (Severe Persistent) RF M all 0.8723404
0.3126896 DAP Exacer vs. followup (Severe Persistent) RF M all 0.8617021
0.2868544 IFI35 Exacer vs. followup (Severe Persistent) RF M all 0.8510638
0.2724368 ATP8A1 Exacer vs. followup (Severe Persistent) RF M all 0.8404255
0.2637813 CTSA Exacer vs. followup (Severe Persistent) RF M all 0.8297872
0.2619913 TNFSF4 Exacer vs. followup (Severe Persistent) RF M all 0.8191489
0.2413308 SELPLG Exacer vs. followup (Severe Persistent) RF M all 0.8085106
0.2396137 PSEN1 Exacer vs. followup (Severe Persistent) RF M all 0.7978723
0.2284318 SF3B1 Exacer vs. followup (Severe Persistent) RF M all 0.7872340
0.2247025 FOS Exacer vs. followup (Severe Persistent) RF M all 0.7765957
0.2222947 IL32 Exacer vs. followup (Severe Persistent) RF M all 0.7659574
0.2033828 CLEC4E Exacer vs. followup (Severe Persistent) RF M all 0.7553191
0.1986217 ABHD5 Exacer vs. followup (Severe Persistent) RF M all 0.7446809
0.1905577 CHP1 Exacer vs. followup (Severe Persistent) RF M all 0.7340426
0.1902909 ITSN1 Exacer vs. followup (Severe Persistent) RF M all 0.7234043
0.1840148 CXCL2 Exacer vs. followup (Severe Persistent) RF M all 0.7127660
0.1798963 LMBRD1 Exacer vs. followup (Severe Persistent) RF M all 0.7021277
0.1774282 TFEB Exacer vs. followup (Severe Persistent) RF M all 0.6914894
0.1715135 PPP3R1 Exacer vs. followup (Severe Persistent) RF M all 0.6808511
0.1690791 SPINK5 Exacer vs. followup (Severe Persistent) RF M all 0.6702128
0.1647629 PELI1 Exacer vs. followup (Severe Persistent) RF M all 0.6595745
0.1639535 MME Exacer vs. followup (Severe Persistent) RF M all 0.6489362
0.1586859 CREBBP Exacer vs. followup (Severe Persistent) RF M all 0.6382979
0.1549825 TGFBI Exacer vs. followup (Severe Persistent) RF M all 0.6276596
0.1548415 PLAU Exacer vs. followup (Severe Persistent) RF M all 0.6170213
0.1532444 TLR7 Exacer vs. followup (Severe Persistent) RF M all 0.6063830
0.1531044 LCN2 Exacer vs. followup (Severe Persistent) RF M all 0.5957447
0.1505563 GNAS Exacer vs. followup (Severe Persistent) RF M all 0.5851064
0.1499424 VCAN Exacer vs. followup (Severe Persistent) RF M all 0.5744681
0.1489139 CD8A Exacer vs. followup (Severe Persistent) RF M all 0.5638298
0.1411545 CDH1 Exacer vs. followup (Severe Persistent) RF M all 0.5531915
0.1401908 MS4A2 Exacer vs. followup (Severe Persistent) RF M all 0.5425532
0.1355880 SMCHD1 Exacer vs. followup (Severe Persistent) RF M all 0.5319149
0.1335883 TIA1 Exacer vs. followup (Severe Persistent) RF M all 0.5212766
0.1333384 LYST Exacer vs. followup (Severe Persistent) RF M all 0.5106383
0.1299377 ATP11A Exacer vs. followup (Severe Persistent) RF M all 0.5000000
0.1254962 ZNF609 Exacer vs. followup (Severe Persistent) RF M all 0.4893617
0.1247461 GNLY Exacer vs. followup (Severe Persistent) RF M all 0.4787234
0.1247456 FOXJ1 Exacer vs. followup (Severe Persistent) RF M all 0.4680851
0.1240788 FUT7 Exacer vs. followup (Severe Persistent) RF M all 0.4574468
0.1225051 MAP3K8 Exacer vs. followup (Severe Persistent) RF M all 0.4468085
0.1221927 IL15RA Exacer vs. followup (Severe Persistent) RF M all 0.4361702
0.1197468 PLXNC1 Exacer vs. followup (Severe Persistent) RF M all 0.4255319
0.1156396 QKI Exacer vs. followup (Severe Persistent) RF M all 0.4148936
0.1108925 LCP1 Exacer vs. followup (Severe Persistent) RF M all 0.4042553
0.1107846 KRT23 Exacer vs. followup (Severe Persistent) RF M all 0.3936170
0.1085751 FPR1 Exacer vs. followup (Severe Persistent) RF M all 0.3829787
0.1081747 FPR2 Exacer vs. followup (Severe Persistent) RF M all 0.3723404
0.1065578 VPS13A Exacer vs. followup (Severe Persistent) RF M all 0.3617021
0.1061351 SULT1A1 Exacer vs. followup (Severe Persistent) RF M all 0.3510638
0.1038340 CXCL10 Exacer vs. followup (Severe Persistent) RF M all 0.3404255
0.1023103 TNFSF10 Exacer vs. followup (Severe Persistent) RF M all 0.3297872
0.0991108 KIAA1551 Exacer vs. followup (Severe Persistent) RF M all 0.3191489
0.0969852 CD4 Exacer vs. followup (Severe Persistent) RF M all 0.3085106
0.0956706 DESI1 Exacer vs. followup (Severe Persistent) RF M all 0.2978723
0.0950325 IFRD1 Exacer vs. followup (Severe Persistent) RF M all 0.2872340
0.0933520 AHCTF1 Exacer vs. followup (Severe Persistent) RF M all 0.2765957
0.0902364 RALGPS2 Exacer vs. followup (Severe Persistent) RF M all 0.2659574
0.0890534 SH3BGRL3 Exacer vs. followup (Severe Persistent) RF M all 0.2553191
0.0850262 RGS2 Exacer vs. followup (Severe Persistent) RF M all 0.2446809
0.0846507 CASP8 Exacer vs. followup (Severe Persistent) RF M all 0.2340426
0.0824195 CD55 Exacer vs. followup (Severe Persistent) RF M all 0.2234043
0.0817161 CTDSP2 Exacer vs. followup (Severe Persistent) RF M all 0.2127660
0.0807123 PTPN18 Exacer vs. followup (Severe Persistent) RF M all 0.2021277
0.0798204 CXCL6 Exacer vs. followup (Severe Persistent) RF M all 0.1914894
0.0798027 MAP3K5 Exacer vs. followup (Severe Persistent) RF M all 0.1808511
0.0787080 NFKBIA Exacer vs. followup (Severe Persistent) RF M all 0.1702128
0.0770730 THY1 Exacer vs. followup (Severe Persistent) RF M all 0.1595745
0.0759150 PABPC1 Exacer vs. followup (Severe Persistent) RF M all 0.1489362
0.0743729 COPB1 Exacer vs. followup (Severe Persistent) RF M all 0.1382979
0.0713779 JAM3 Exacer vs. followup (Severe Persistent) RF M all 0.1276596
0.0697145 GBE1 Exacer vs. followup (Severe Persistent) RF M all 0.1170213
0.0696900 IL1R1 Exacer vs. followup (Severe Persistent) RF M all 0.1063830
0.0622675 SH2B2 Exacer vs. followup (Severe Persistent) RF M all 0.0957447
0.0590771 F13A1 Exacer vs. followup (Severe Persistent) RF M all 0.0851064
0.0572345 PPBP Exacer vs. followup (Severe Persistent) RF M all 0.0744681
0.0562168 ZNF185 Exacer vs. followup (Severe Persistent) RF M all 0.0638298
0.0547922 ZNF281 Exacer vs. followup (Severe Persistent) RF M all 0.0531915
0.0502393 IL1R2 Exacer vs. followup (Severe Persistent) RF M all 0.0425532
0.0490545 ULBP2 Exacer vs. followup (Severe Persistent) RF M all 0.0319149
0.0480472 SEMA4D Exacer vs. followup (Severe Persistent) RF M all 0.0212766
0.0442305 ITGA2B Exacer vs. followup (Severe Persistent) RF M all 0.0106383
0.0420836 IL26 Exacer vs. followup (Severe Persistent) RF M all 0.0000000

Asthma severity

Train PLS-DA models (severity)

# all_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_plsda(eset_list = esetList, pheno_list = phenoDataList, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]])
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# pheno = lapply(phenoDataList, function(i){subset(i, sex == "F")})
# f_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_plsda(eset_list = esetList, pheno_list = pheno, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]])
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# pheno = lapply(phenoDataList, function(i){subset(i, sex == "M")})
# m_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_plsda(eset_list = esetList, pheno_list = pheno, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]])
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# 
# ## perf
# sev_plsda_df <- rbind(do.call(rbind, all_sev$df) %>% mutate(sex="M+F"),
#       do.call(rbind, f_sev$df) %>% mutate(sex="F"),
#       do.call(rbind, m_sev$df) %>% mutate(sex="M"))
# sev_plsda_df$sampletype[sev_plsda_df$sampletype == "balf"] <- "BALF"
# 
# ## feature importance
# sev_plsda_feat <- rbind(do.call(rbind, all_sev$feat) %>% mutate(sex="M+F"),
#       do.call(rbind, f_sev$feat) %>% mutate(sex="F"),
#       do.call(rbind, m_sev$feat) %>% mutate(sex="M"))
# sev_plsda_feat$sampletype[sev_plsda_feat$sampletype == "balf"] <- "BALF"
# sev_plsda <- list(feat = sev_plsda_feat, df = sev_plsda_df)
# 
# saveRDS(sev_plsda, here("results", "sev_plsda.rds"))

Train RF models (severity)

# all_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_rf(eset_list = esetList, pheno_list = phenoDataList, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]], workers = 8)
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# pheno = lapply(phenoDataList, function(i){subset(i, sex == "F")})
# f_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_rf(eset_list = esetList, pheno_list = pheno, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]], workers = 8)
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# pheno = lapply(phenoDataList, function(i){subset(i, sex == "M")})
# m_sev <- lapply(names(latephase_biomarkers), function(i){
#   res <- lar_rf(eset_list = esetList, pheno_list = pheno, gse_list = select_gse,
#                      biomarkers = latephase_biomarkers[[i]], workers = 8)
#   list(feat = do.call(rbind, res$feat) %>% mutate(panel = i),
#        df = do.call(rbind, res$df) %>% mutate(panel = i))
# }) %>%
#   zip_nPure()
# 
# ## perf
# sev_rf_df <- rbind(do.call(rbind, all_sev$df) %>% mutate(sex="M+F"),
#       do.call(rbind, f_sev$df) %>% mutate(sex="F"),
#       do.call(rbind, m_sev$df) %>% mutate(sex="M"))
# sev_rf_df$sampletype[sev_rf_df$sampletype == "balf"] <- "BALF"
# 
# ## feature importance
# sev_rf_feat <- rbind(do.call(rbind, all_sev$feat) %>% mutate(sex="M+F"),
#       do.call(rbind, f_sev$feat) %>% mutate(sex="F"),
#       do.call(rbind, m_sev$feat) %>% mutate(sex="M"))
# sev_rf_feat$sampletype[sev_rf_feat$sampletype == "balf"] <- "BALF"
# sev_rf <- list(feat = sev_rf_feat, df = sev_rf_df)
# 
# saveRDS(sev_rf, here("results", "sev_rf.rds"))

Plot model performance heatmap (severity)

sev_plsda <- readRDS(here("results", "sev_plsda.rds"))
sev_rf <- readRDS(here("results", "sev_rf.rds"))
col_names <- intersect(colnames(sev_rf$df), colnames(sev_plsda$df))
panel_names <- c("all", "panCancer", "UCSC_isoforms", "UCSC", "Ensembl", "Trinity")
auc <- rbind(sev_rf$df[, col_names],
             sev_plsda$df[, col_names]) %>% 
  filter(stat == "AUC.mean") %>% 
  dplyr::select(-stat) %>% 
  mutate(model_panel = paste(model, panel, sep="_")) %>% 
  dplyr::select(-c(model, panel)) %>% 
  spread(model_panel, value)

auc2 <- auc[, -c(1:4)]
classifer <- factor(sapply(strsplit(colnames(auc2), "_"), function(i) i[[1]]), 
                    c("PLSDA", "RF"))
colnames(auc2) <- sapply(strsplit(colnames(auc2), "_"), function(i) i[[2]])
row_ha <- rowAnnotation(sampletype=auc$sampletype,
                        comparison=auc$comparison, sex=auc$sex,
                        col = list(sampletype = c("airway"="#DEEBF7","BALF"="#9ECAE1","induced sputum"="#4292C6", "blood" = "red"),
                                   comparison = c("healthyControls_vs_moderateAsthma"="#E69F00", "healthyControls_vs_severeAsthma"="#56B4E9", "moderateAsthma_vs_severeAsthma"="#009E73"),
                                   sex = c("F"="#80CDC1","M"="#35978F","M+F"="#01665E")))

h2 <- Heatmap(auc2, column_split = classifer,
        right_annotation = row_ha, 
        cluster_columns = TRUE,
        border = TRUE, name="AUC",
    cell_fun = function(j, i, x, y, width, height, fill) {
        if(auc2[i, j] > 0.9) {
          grid.text("***", x, y, gp = gpar(fontsize = 15))
        } else if(auc2[i, j] > 0.8) {
          grid.text("**", x, y, gp = gpar(fontsize = 15))
        } else if(auc2[i, j] > 0.7) {
          grid.text("*", x, y, gp = gpar(fontsize = 15))
        }
})
h2

Summarize model performance table (severity)

sevtable <- rbind(sev_rf$df[, col_names],
             sev_plsda$df[, col_names]) %>% 
  mutate(value = signif(value, 2)) %>%  
  filter(stat == "AUC.mean") %>% 
  spread(model, value) %>% 
  filter(PLSDA > 0.7) %>% 
  filter(RF > 0.7)
write.csv(sevtable, here::here("results", "sev_models_perfs.csv"))

sevtable %>% 
  group_by(sampletype, comparison, sex) %>% 
  summarise(count = n()) %>% 
  spread(sampletype, count)
## # A tibble: 9 × 6
## # Groups:   comparison [3]
##   comparison                        sex   airway  BALF blood `induced sputum`
##   <chr>                             <chr>  <int> <int> <int>            <int>
## 1 healthyControls_vs_moderateAsthma F          5    NA    NA               NA
## 2 healthyControls_vs_moderateAsthma M          2     5    NA                2
## 3 healthyControls_vs_moderateAsthma M+F        5     4    NA               NA
## 4 healthyControls_vs_severeAsthma   F          5     6    NA                3
## 5 healthyControls_vs_severeAsthma   M          4     6     3                5
## 6 healthyControls_vs_severeAsthma   M+F        6     6     3                5
## 7 moderateAsthma_vs_severeAsthma    F         NA     6    NA                2
## 8 moderateAsthma_vs_severeAsthma    M         NA     6    NA                1
## 9 moderateAsthma_vs_severeAsthma    M+F       NA     6    NA                5

Compile feature importance + rank summaries

selectcols <- intersect(colnames(sev_plsda$feat), colnames(sev_rf$feat))
sevfeat <- rbind(sev_plsda$feat[, selectcols], 
                 sev_rf$feat[,selectcols]) %>% 
  right_join(sevtable, by=c("gse", "comparison", "panel", "sex", "sampletype")) %>% 
  dplyr::select(-c(stat, PLSDA, RF, gse)) %>% 
  group_by(comparison, panel, sex, model, sampletype) %>%
  mutate(rank_pct = percent_rank(importance))

exacer_rank <- exacerfeat %>%
  group_by(feature, comparison) %>%
  summarise(
   avg_rank = mean(rank_pct, na.rm = TRUE),
   sd_rank = sd(rank_pct, na.rm = TRUE),
   .groups   = "drop"
  )
sev_rank <- sevfeat %>%
  group_by(feature, comparison, sampletype) %>%
  summarise(
   avg_rank = mean(rank_pct, na.rm = TRUE),
   sd_rank = sd(rank_pct, na.rm = TRUE),
    .groups   = "drop"
  )

Pathway annotation + pathway barplots (assigned/unassigned)

# sev_rank is your tibble with feature, avg_rank, sd_rank

# pick a KEGG library available in Enrichr
dbs <- enrichR::listEnrichrDbs()
kegg_db <- dbs$libraryName[grepl("KEGG", dbs$libraryName)][1]
kegg_db
## [1] "KEGG_2013"
# e.g. "KEGG_2021_Human" (depends on what's available)

# run enrichr
db <- "GO_Biological_Process_2025"
enr <- enrichR::enrichr(latephase_biomarkers$all, databases = db)
## Uploading data to Enrichr... Done.
##   Querying GO_Biological_Process_2025... Done.
## Parsing results... Done.
kegg <- enr[[db]]

# keep significant-ish terms (tune as you like)
kegg_sig <- kegg %>%
  filter(Adjusted.P.value <= 0.1) %>%
  arrange(Adjusted.P.value)

# parse the "Genes" column from enrichr (overlapping genes per pathway)
gene_path_long <- kegg_sig %>%
  dplyr::select(Pathway = Term, padj = Adjusted.P.value, Genes) %>%
  mutate(Genes = str_split(Genes, pattern = ";\\s*")) %>%
  unnest(Genes) %>%
  dplyr::rename(feature = Genes)

# assign each gene to ONE pathway:
# (the pathway with smallest adjusted p among those containing the gene)
gene2path <- gene_path_long %>%
  group_by(feature) %>%
  slice_min(order_by = padj, n = 1, with_ties = FALSE) %>%
  ungroup()

# attach pathway to your ranking table
exacer_annot <- exacer_rank %>%
  left_join(gene2path %>% dplyr::select(feature, Pathway), by = "feature") %>%
  mutate(Pathway = ifelse(is.na(Pathway), "Unassigned", Pathway)) %>% 
  mutate(sampletype = "PBMCs") %>% 
  mutate(comparison = factor(comparison, c("Exacer vs. Quiet (Moderate Persistent)", "Exacer vs. Quiet (Severe Persistent)", "Exacer vs. followup (Moderate Persistent)", "Exacer vs. followup (Severe Persistent)")))
exacer_annot %>% head()
## # A tibble: 6 × 6
##   feature comparison                         avg_rank sd_rank Pathway sampletype
##   <chr>   <fct>                                 <dbl>   <dbl> <chr>   <chr>     
## 1 ABHD5   Exacer vs. Quiet (Severe Persiste…   0.320   0.128  Negati… PBMCs     
## 2 ABHD5   Exacer vs. followup (Moderate Per…   0.0979  0.0837 Negati… PBMCs     
## 3 ABHD5   Exacer vs. followup (Severe Persi…   0.798   0.0752 Negati… PBMCs     
## 4 AHCTF1  Exacer vs. Quiet (Severe Persiste…   0.675   0.0995 Unassi… PBMCs     
## 5 AHCTF1  Exacer vs. followup (Moderate Per…   0.545   0.216  Unassi… PBMCs     
## 6 AHCTF1  Exacer vs. followup (Severe Persi…   0.193   0.0829 Unassi… PBMCs
# attach pathway to your ranking table
sev_annot <- sev_rank %>%
  left_join(gene2path %>% dplyr::select(feature, Pathway), by = "feature") %>%
  mutate(Pathway = ifelse(is.na(Pathway), "Unassigned", Pathway))
sev_annot %>% head()
## # A tibble: 6 × 6
##   feature comparison                        sampletype  avg_rank sd_rank Pathway
##   <chr>   <chr>                             <chr>          <dbl>   <dbl> <chr>  
## 1 ABHD5   healthyControls_vs_moderateAsthma BALF           0.979  0.0180 Negati…
## 2 ABHD5   healthyControls_vs_moderateAsthma airway         0.293  0.187  Negati…
## 3 ABHD5   healthyControls_vs_moderateAsthma induced sp…    0.340  0.256  Negati…
## 4 ABHD5   healthyControls_vs_severeAsthma   BALF           0.704  0.173  Negati…
## 5 ABHD5   healthyControls_vs_severeAsthma   airway         0.291  0.191  Negati…
## 6 ABHD5   healthyControls_vs_severeAsthma   blood          0.694  0.272  Negati…

Assemble multi-panel Figure 4

p1_unassigned <- plot_varimp_pathways(
  exacer_annot,
  top_n = 30,
  sum_threshold = 1.5,
  include_unassigned = TRUE
) + theme(legend.position = "top") +
  scale_fill_manual(values = c("Exacer vs. Quiet (Moderate Persistent)"="#DEEBF7", "Exacer vs. Quiet (Severe Persistent)"="#9ECAE1", "Exacer vs. followup (Moderate Persistent)"="#4292C6", "Exacer vs. followup (Severe Persistent)"="#084594"))
p1_unassigned

p1_assigned <- plot_varimp_pathways(
  exacer_annot,
  top_n = 20,
  sum_threshold = 1.5,
  include_unassigned = FALSE
) + theme(legend.position = "top") +
  scale_fill_manual(values = c("Exacer vs. Quiet (Moderate Persistent)"="#DEEBF7", "Exacer vs. Quiet (Severe Persistent)"="#9ECAE1", "Exacer vs. followup (Moderate Persistent)"="#4292C6", "Exacer vs. followup (Severe Persistent)"="#084594"))
p1_assigned

p2_unassigned <- plot_varimp_pathways(
  sev_annot,
  top_n = 10,
  sum_threshold = 2,
  include_unassigned = TRUE
) + theme(legend.position = "top") +
  scale_fill_manual(values = c("healthyControls_vs_moderateAsthma"="#E69F00", "healthyControls_vs_severeAsthma"="#56B4E9", "moderateAsthma_vs_severeAsthma"="#009E73"))
p2_unassigned

p2_assigned <- plot_varimp_pathways(
  sev_annot,
  top_n = 10,
  sum_threshold = 2,
  include_unassigned = FALSE
) + theme(legend.position = "top") +
  scale_fill_manual(values = c("healthyControls_vs_moderateAsthma"="#E69F00", "healthyControls_vs_severeAsthma"="#56B4E9", "moderateAsthma_vs_severeAsthma"="#009E73"))
p2_assigned

ggsave(here("results", "Figure4b1.png"), plot = p1_unassigned, width = 3, height = 5)
ggsave(here("results", "Figure4b2.png"), plot = p1_assigned, width = 12, height = 5)
ggsave(here("results", "Figure4d1.png"), plot = p2_unassigned, width = 10, height = 5)
ggsave(here("results", "Figure4d2.png"), plot = p2_assigned, width = 10, height = 5)

save panels of Figure 4

library(grid)
library(patchwork)
library(ComplexHeatmap)

g1 <- grid.grabExpr(draw(h1, merge_legends = FALSE))
g2 <- grid.grabExpr(draw(h2, merge_legends = FALSE))
ggsave(here("results", "Figure4a.png"), plot = g1, width = 10, height = 5)
ggsave(here("results", "Figure4b.png"), plot = p1_assigned, width = 10, height = 5)
ggsave(here("results", "Figure4c.png"), plot = g2, width = 10, height = 7)
ggsave(here("results", "Figure4d.png"), plot = p2_assigned, width = 10, height = 7)

Check top transcripts in male panel

male_features <- exacerfeat %>% 
  ungroup() %>% 
  group_by(feature, comparison) %>% 
  filter(sex == "M") %>% 
  summarise(avg = mean(rank_pct)) %>% 
  arrange(desc(avg)) %>% 
  ungroup() %>% 
  group_by(comparison) %>% 
  dplyr::slice(1:2) %>%
  mutate(
    severity = sub("^.*\\((.*)\\)\\s*$", "\\1", comparison)       # text inside ()
  )

plots <- mapply(function(x, y){
    res = plot_gene_sex_lme(gene = x,
           severity = y,
           geoPanelGenes = geoPanelGenes,
           phenoDataList = phenoDataList)
  res$plot
}, x = male_features$feature, y = male_features$severity)


male_plots <- plot_grid(plotlist = plots)
ggsave(here("results", "male_specific_biomarkers.png"), male_plots,
       width = 10, height = 7)
male_plots

sessionInfo

sessionInfo()
## R version 4.5.1 (2025-06-13)
## Platform: x86_64-apple-darwin20
## Running under: macOS Ventura 13.6.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/Vancouver
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] patchwork_1.3.2       future.apply_1.20.0   future_1.67.0        
##  [4] ranger_0.17.0         pROC_1.19.0.1         cowplot_1.2.0        
##  [7] UpSetR_1.4.0          ggrepel_0.9.6         enrichR_3.4          
## [10] here_1.0.2            ComplexHeatmap_2.26.0 mixOmics_6.34.0      
## [13] lattice_0.22-7        MASS_7.3-65           limma_3.66.0         
## [16] nlme_3.1-168          lubridate_1.9.4       forcats_1.0.1        
## [19] stringr_1.6.0         dplyr_1.1.4           purrr_1.1.0          
## [22] readr_2.1.6           tidyr_1.3.1           tibble_3.3.0         
## [25] ggplot2_4.0.1         tidyverse_2.0.0      
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3  rstudioapi_0.17.1   jsonlite_2.0.0     
##   [4] shape_1.4.6.1       magrittr_2.0.4      estimability_1.5.1 
##   [7] magick_2.9.0        farver_2.1.2        nloptr_2.2.1       
##  [10] rmarkdown_2.30      GlobalOptions_0.1.2 ragg_1.5.0         
##  [13] vctrs_0.6.5         Cairo_1.7-0         minqa_1.2.8        
##  [16] rstatix_0.7.3       htmltools_0.5.8.1   curl_7.0.0         
##  [19] broom_1.0.10        janeaustenr_1.0.0   Formula_1.2-5      
##  [22] sass_0.4.10         parallelly_1.45.1   bslib_0.9.0        
##  [25] tokenizers_0.3.0    pbkrtest_0.5.5      plyr_1.8.9         
##  [28] emmeans_2.0.1       cachem_1.1.0        commonmark_2.0.0   
##  [31] igraph_2.2.1        lifecycle_1.0.4     iterators_1.0.14   
##  [34] pkgconfig_2.0.3     Matrix_1.7-3        R6_2.6.1           
##  [37] fastmap_1.2.0       rbibutils_2.4       clue_0.3-66        
##  [40] numDeriv_2016.8-1.1 digest_0.6.37       tidytext_0.4.3     
##  [43] colorspace_2.1-2    rARPACK_0.11-0      S4Vectors_0.48.0   
##  [46] rprojroot_2.1.1     RSpectra_0.16-2     textshaping_1.0.4  
##  [49] ellipse_0.5.0       SnowballC_0.7.1     ggpubr_0.6.2       
##  [52] WriteXLS_6.8.0      labeling_0.4.3      timechange_0.3.0   
##  [55] abind_1.4-8         httr_1.4.7          compiler_4.5.1     
##  [58] withr_3.0.2         doParallel_1.0.17   backports_1.5.0    
##  [61] S7_0.2.0            BiocParallel_1.44.0 carData_3.0-5      
##  [64] ggsignif_0.6.4      rjson_0.2.23        corpcor_1.6.10     
##  [67] tools_4.5.1         glue_1.8.0          gridtext_0.1.5     
##  [70] cluster_2.1.8.1     reshape2_1.4.4      generics_0.1.4     
##  [73] gtable_0.3.6        tzdb_0.5.0          hms_1.1.4          
##  [76] car_3.1-3           xml2_1.4.1          utf8_1.2.6         
##  [79] BiocGenerics_0.56.0 foreach_1.5.2       pillar_1.11.1      
##  [82] markdown_2.0        circlize_0.4.16     splines_4.5.1      
##  [85] ggtext_0.1.2        tidyselect_1.2.1    knitr_1.50         
##  [88] reformulas_0.4.2    gridExtra_2.3       litedown_0.8       
##  [91] IRanges_2.44.0      stats4_4.5.1        xfun_0.54          
##  [94] statmod_1.5.1       matrixStats_1.5.0   stringi_1.8.7      
##  [97] yaml_2.3.12         boot_1.3-31         evaluate_1.0.5     
## [100] codetools_0.2-20    cli_3.6.5           xtable_1.8-4       
## [103] systemfonts_1.3.1   Rdpack_2.6.4        jquerylib_0.1.4    
## [106] Rcpp_1.1.0          globals_0.18.0      coda_0.19-4.1      
## [109] png_0.1-8           parallel_4.5.1      lme4_1.1-37        
## [112] listenv_0.10.0      mvtnorm_1.3-3       lmerTest_3.1-3     
## [115] scales_1.4.0        crayon_1.5.3        GetoptLong_1.0.5   
## [118] rlang_1.1.6